def load_config(config, required_keys=None):
""" Read in the config file, print a logging (INFO) statement and verify
that the required keys are present
"""
import yaml
msg = "Reading config file"
logger.info(msg)
config = yaml.load(open(config))
if required_keys is not None:
utils.check_keys_exist(config, required_keys)
return config
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script runs the Rp-Bp and Rp-chi pipelines on a given sample. "
"It requires a YAML config file that includes a number of keys. Please see the "
"documentation for a complete description.")
parser.add_argument('raw_data', help="The raw data file (fastq[.gz])")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('name', help="The name for the dataset, used in the created files")
parser.add_argument('--tmp', help="The temp directory", default=default_tmp)
parser.add_argument('--flexbar-options', help="A space-delimited list of options to"
"pass to flexbar. Each option must be quoted separately as in \"--flexbarOption value\""
"If specified, flexbar options will override default settings.", nargs='*', type=str)
parser.add_argument('--overwrite', help="If this flag is present, existing files "
"will be overwritten.", action='store_true')
parser.add_argument('--profiles-only', help="If this flag is present, then only "
"the ORF profiles will be created", action='store_true')
parser.add_argument('-k', '--keep-intermediate-files', help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.", action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar',
args.star_executable,
'samtools',
'bowtie2',
'create-base-genome-profile',
'remove-multimapping-reads',
'extract-metagene-profiles',
'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets',
'extract-orf-profiles',
'estimate-orf-bayes-factors',
'select-final-prediction-set',
'create-orf-profiles',
'predict-translated-orfs'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data',
'ribosomal_index',
'star_index',
'genome_base_path',
'genome_name',
'fasta',
'gtf'
]
utils.check_keys_exist(config, required_keys)
# now, check if we want to use slurm
msg = "use_slurm: {}".format(args.use_slurm)
logger.debug(msg)
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
note_str = config.get('note', None)
# the first step is the standard riboseq preprocessing
# handle do_not_call so that we _do_ call the preprocessing script,
# but that it does not run anything
do_not_call_str = ""
if not call:
do_not_call_str = "--do-not-call"
overwrite_str = ""
if args.overwrite:
overwrite_str = "--overwrite"
# for a sample, we first create its filtered genome profile
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_option_str = ""
if args.flexbar_options is not None:
flexbar_option_str = "--flexbar-options {}".format(' '.join('"' + flx_op + '"'
for flx_op in args.flexbar_options))
mem_str = "--mem {}".format(shlex.quote(args.mem))
cmd = ("create-orf-profiles {} {} {} --num-cpus {} {} {} {} {} {} {} {} {}".format(args.raw_data,
args.config, args.name, args.num_cpus, mem_str, do_not_call_str, overwrite_str,
logging_str, star_str, tmp_str, flexbar_option_str, keep_intermediate_str))
shell_utils.check_call(cmd)
# check if we only want to create the profiles
if args.profiles_only:
return
# then we predict the ORFs
cmd = ("predict-translated-orfs {} {} --num-cpus {} {} {} {}".format(args.config,
args.name, args.num_cpus, do_not_call_str, overwrite_str, logging_str))
shell_utils.check_call(cmd)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script creates the plots which detail the basic characteristics "
"of the ORF predictions from the Rp-Bp pipeline. It also creates and compiles (if "
"possible) a latex report for them.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('out', help="The base output directory for the latex report")
parser.add_argument('--show-unfiltered-orfs', help="If this flag is "
"present, bar charts showing the distribution of the types of the "
"unfiltered ORF set will be included", action='store_true')
parser.add_argument('--show-orf-periodicity', help="If this flag is "
"present, bar charts showing the periodicity of each ORF type will be "
"included in the report.", action='store_true')
parser.add_argument('--uniprot', help="The uniprot ORF lengths, if available",
default=default_uniprot)
parser.add_argument('--uniprot-label', help="The label to use for the uniprot ORFs in "
"the plot", default=default_uniprot_label)
parser.add_argument('--image-type', help="The format of the image files. This must be "
"a format usable by matplotlib.", default=default_image_type)
parser.add_argument('--overwrite', help="If this flag is present, existing files will "
"be overwritten.", action='store_true')
parser.add_argument('--note', help="If this option is given, it will be used in the "
"filenames.\n\nN.B. This REPLACES the note in the config file.", default=default_note)
parser.add_argument('--show-chisq', help="If this flag is given, then the "
"results from Rp-chi will be included in the document; otherwise, they "
"will not be created or shown.", action='store_true')
parser.add_argument('-t', '--tmp', help="A location for temporary files",
default=default_tmp)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
config = yaml.load(open(args.config))
# keep multimappers?
is_unique = not ('keep_riboseq_multimappers' in config)
programs = [
'create-orf-length-distribution-line-graph',
'create-orf-types-bar-chart',
'visualize-orf-type-metagene-profiles'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data',
'riboseq_samples'
]
utils.check_keys_exist(config, required_keys)
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
# by default, we will not include chisq
chisq_values = [False]
if args.show_chisq:
chisq_values = [True, False]
filtered_values = [True]
if args.show_unfiltered_orfs:
filtered_values = [True, False]
grouped_values = [True, False]
# make sure the path to the output file exists
os.makedirs(args.out, exist_ok=True)
# first, create all of the figures
create_all_figures(config, args)
note_str = config.get('note', None)
out_note_str = note_str
if args.note is not None and len(args.note) > 0:
out_note_str = args.note
fraction = config.get('smoothing_fraction', None)
reweighting_iterations = config.get('smoothing_reweighting_iterations', None)
project_name = config.get("project_name", default_project_name)
title = "Rp-Bp prediction analysis for {}".format(project_name)
abstract = "This document shows the results of the Rp-Bp pipeline analysis."
#tex_file = os.path.join(args.out, "prediction-report.tex")
tex_file = filenames.get_rpbp_prediction_report(args.out, out_note_str)
with open(tex_file, 'w') as out:
latex.begin_document(out, title, abstract)
latex.write(out, "\n")
latex.clearpage(out)
### ORF type distributions
title = "Predicted ORF type distributions"
latex.section(out, title)
# first, handle all of the regular datasets
sample_names = sorted(config['riboseq_samples'].keys())
# and check if we also have replicates
replicate_names = []
if 'riboseq_biological_replicates' in config:
replicate_names = sorted(ribo_utils.get_riboseq_replicates(config).keys())
strands = ["+", "-"]
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = ("Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF types: {}".format(sample_name)
is_first = True
# first, just dump all of the bar charts to the page
it = itertools.product(grouped_values, chisq_values, filtered_values)
for is_grouped, is_chisq, is_filtered in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_types_bar_chart = filenames.get_orf_types_bar_chart(
config['riboseq_data'],
sample_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq,
is_filtered=is_filtered
)
msg = "Looking for image file: {}".format(orf_types_bar_chart)
logger.debug(msg)
if os.path.exists(orf_types_bar_chart):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_types_bar_chart, height=0.15)
if i%6 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_types_bar_chart)
logger.warning(msg)
if (i > 0) and (i%6) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%6 != 0:
latex.clearpage(out)
# now, if the config file specifies replicates, create figures for those
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF types: {}".format(replicate_name)
it = itertools.product(grouped_values, chisq_values, filtered_values)
is_first = True
for is_grouped, is_chisq, is_filtered in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_types_bar_chart = filenames.get_orf_types_bar_chart(
config['riboseq_data'],
replicate_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq,
is_filtered=is_filtered
)
msg = "Looking for image file: {}".format(orf_types_bar_chart)
logger.debug(msg)
if os.path.exists(orf_types_bar_chart):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_types_bar_chart, height=0.15)
if i%6 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_types_bar_chart)
logger.warning(msg)
if (i > 0) and (i%6) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%6 != 0:
latex.clearpage(out)
### ORF type length distributions
title = "Predicted ORF type length distributions"
latex.section(out, title)
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = ("Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF type length distributions: {}".format(sample_name)
is_first = True
it = itertools.product(grouped_values, chisq_values)
for is_grouped, is_chisq in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_length_line_graph = filenames.get_orf_length_distribution_line_graph(
config['riboseq_data'],
sample_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq
)
if os.path.exists(orf_length_line_graph):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_length_line_graph, height=0.15)
if i%4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_length_line_graph)
logger.debug(msg)
if (i > 0) and (i%4) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%4 != 0:
latex.clearpage(out)
# now, if the config file specifies replicates, create figures for those
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF types: {}".format(replicate_name)
is_first = True
it = itertools.product(grouped_values, chisq_values)
for is_grouped, is_chisq in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_length_line_graph = filenames.get_orf_length_distribution_line_graph(
config['riboseq_data'],
replicate_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq
)
if os.path.exists(orf_length_line_graph):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_length_line_graph, height=0.15)
if i%4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_length_line_graph)
logger.debug(msg)
if (i > 0) and (i%4) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%4 != 0:
latex.clearpage(out)
### ORF type metagene profiles
if args.show_orf_periodicity:
title = "Predicted ORF type metagene profiles"
latex.section(out, title)
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = ("Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF type metagene profiles: {}".format(sample_name)
is_first = True
for is_chisq in chisq_values:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_type_profile_base = filenames.get_orf_type_profile_base(
config['riboseq_data'],
sample_name,
length=lengths, offset=offsets,
is_unique=is_unique,
note=out_note_str,
fraction=f, reweighting_iterations=rw,
is_chisq=is_chisq)
it = itertools.product(ribo_utils.orf_types, strands)
for orf_type, strand in it:
orf_type_profile = filenames.get_orf_type_profile_image(
orf_type_profile_base,
orf_type,
strand,
args.image_type
)
msg = "Looking for image file: {}".format(orf_type_profile)
logger.debug(msg)
if os.path.exists(orf_type_profile):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_type_profile, height=0.23)
if i%4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_type_profile)
logger.warning(msg)
if (i > 0) and (i%4 != 0):
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%4 != 0:
latex.clearpage(out)
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF type metagene profiles: {}".format(replicate_name)
is_first = True
for is_chisq in chisq_values:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_type_profile_base = filenames.get_orf_type_profile_base(
config['riboseq_data'],
replicate_name,
length=lengths, offset=offsets,
is_unique=is_unique,
note=out_note_str,
fraction=f, reweighting_iterations=rw,
is_chisq=is_chisq
)
it = itertools.product(ribo_utils.orf_types, strands)
for orf_type, strand in it:
orf_type_profile = filenames.get_orf_type_profile_image(
orf_type_profile_base,
orf_type,
strand,
args.image_type
)
if os.path.exists(orf_type_profile):
if is_first or (i%4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_type_profile, height=0.23)
if i % 4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(orf_type_profile)
logger.debug(msg)
if (i > 0) and (i%4 != 0):
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i%4 != 0:
latex.clearpage(out)
latex.end_document(out)
tex_filename = os.path.basename(tex_file)
latex.compile(args.out, tex_filename)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="") #filenames.run_riboseq_preprocessing_description)
parser.add_argument('raw_data', help="The raw data file (fastq[.gz])")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument(
'name', help="The name for the dataset, used in the created files")
parser.add_argument('-p',
'--num-cpus',
help="The number of processors to use",
type=int,
default=default_num_cpus)
parser.add_argument('--mem',
help="The amount of RAM to request",
default=default_mem)
parser.add_argument(
'--flexbar-format-option',
help="The name of the \"format\" "
"option for flexbar. This changed from \"format\" to \"qtrim-format\" in "
"version 2.7.",
default=default_flexbar_format_option)
parser.add_argument('-t',
'--tmp',
help="The location for temporary files. If not "
"specified, program-specific temp locations are used.",
default=default_tmp)
parser.add_argument('--do-not-call', action='store_true')
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
parser.add_argument(
'-k',
'--keep-intermediate-files',
help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.",
action='store_true')
star_utils.add_star_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
msg = "[create-base-genome-profile]: {}".format(' '.join(sys.argv))
logger.info(msg)
config = yaml.load(open(args.config))
call = not args.do_not_call
keep_delete_files = args.keep_intermediate_files or args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar', args.star_executable, 'samtools', 'bowtie2',
'remove-multimapping-reads'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data', 'ribosomal_index', 'gtf', 'genome_base_path',
'genome_name'
]
utils.check_keys_exist(config, required_keys)
note = config.get('note', None)
# Step 0: Running flexbar to remove adapter sequences
raw_data = args.raw_data
flexbar_target = filenames.get_without_adapters_base(
config['riboseq_data'], args.name, note=note)
without_adapters = filenames.get_without_adapters_fastq(
config['riboseq_data'], args.name, note=note)
adapter_seq_str = utils.get_config_argument(config, 'adapter_sequence',
'adapter-seq')
adapter_file_str = utils.get_config_argument(config, 'adapter_file',
'adapters')
quality_format_str = utils.get_config_argument(
config,
'quality_format',
args.flexbar_format_option,
default=default_quality_format)
max_uncalled_str = utils.get_config_argument(config,
'max_uncalled',
default=default_max_uncalled)
pre_trim_left_str = utils.get_config_argument(
config, 'pre_trim_left', default=default_pre_trim_left)
cmd = "flexbar {} {} {} {} -n {} {} -r {} -t {} {}".format(
quality_format_str, max_uncalled_str, adapter_seq_str,
adapter_file_str, args.num_cpus, flexbar_compression_str, raw_data,
flexbar_target, pre_trim_left_str)
in_files = [raw_data]
out_files = [without_adapters]
file_checkers = {without_adapters: fastx_utils.check_fastq_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
# Step 1: Running bowtie2 to remove rRNA alignments
out = utils.abspath("dev", "null") # we do not care about the alignments
without_rrna = filenames.get_without_rrna_fastq(config['riboseq_data'],
args.name,
note=note)
with_rrna = filenames.get_with_rrna_fastq(config['riboseq_data'],
args.name,
note=note)
cmd = "bowtie2 -p {} --very-fast -x {} -U {} -S {} --un-gz {} --al-gz {}".format(
args.num_cpus, config['ribosomal_index'], without_adapters, out,
without_rrna, with_rrna)
in_files = [without_adapters]
in_files.extend(bio.get_bowtie2_index_files(config['ribosomal_index']))
out_files = [without_rrna, with_rrna]
to_delete = [without_adapters]
file_checkers = {without_rrna: fastx_utils.check_fastq_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call,
keep_delete_files=keep_delete_files,
to_delete=to_delete)
# Step 2: Running STAR to align rRNA-depleted reads to genome
star_output_prefix = filenames.get_riboseq_bam_base(config['riboseq_data'],
args.name,
note=note)
#transcriptome_bam = "{}{}".format(star_output_prefix, "Aligned.toTranscriptome.out.bam")
genome_star_bam = "{}{}".format(star_output_prefix,
"Aligned.sortedByCoord.out.bam")
star_compression_str = "--readFilesCommand {}".format(
shlex.quote(args.star_read_files_command))
align_intron_min_str = utils.get_config_argument(
config,
'align_intron_min',
'alignIntronMin',
default=default_align_intron_min)
align_intron_max_str = utils.get_config_argument(
config,
'align_intron_max',
'alignIntronMax',
default=default_align_intron_max)
out_filter_mismatch_n_max_str = utils.get_config_argument(
config,
'out_filter_mismatch_n_max',
'outFilterMismatchNmax',
default=default_out_filter_mismatch_n_max)
out_filter_mismatch_n_over_l_max_str = utils.get_config_argument(
config,
'out_filter_mismatch_n_over_l_max',
'outFilterMismatchNoverLmax',
default=default_out_filter_mismatch_n_over_l_max)
out_filter_type_str = utils.get_config_argument(
config,
'out_filter_type',
'outFilterType',
default=default_out_filter_type)
out_filter_intron_motifs_str = utils.get_config_argument(
config,
'out_filter_intron_motifs',
'outFilterIntronMotifs',
default=default_out_filter_intron_motifs)
out_sam_attributes_str = utils.get_config_argument(
config,
'out_sam_attributes',
'outSAMattributes',
default=default_out_sam_attributes)
star_tmp_str = ""
if args.tmp is not None:
star_tmp_name = "STAR_rpbp"
star_tmp_dir = star_utils.create_star_tmp(args.tmp, star_tmp_name)
star_tmp_str = "--outTmpDir {}".format(star_tmp_dir)
mem_bytes = utils.human2bytes(args.mem)
star_mem_str = "--limitBAMsortRAM {}".format(mem_bytes)
cmd = (
"{} --runThreadN {} {} --genomeDir {} --sjdbGTFfile {} --readFilesIn {} "
"{} {} {} {} {} {} {} {} --outFileNamePrefix {} {} {} {}".format(
args.star_executable, args.num_cpus, star_compression_str,
config['star_index'], config['gtf'], without_rrna,
align_intron_min_str, align_intron_max_str,
out_filter_mismatch_n_max_str, out_filter_type_str,
out_filter_intron_motifs_str, quant_mode_str,
out_filter_mismatch_n_over_l_max_str, out_sam_attributes_str,
star_output_prefix, star_out_str, star_tmp_str, star_mem_str))
in_files = [without_rrna]
in_files.extend(star_utils.get_star_index_files(config['star_index']))
#out_files = [transcriptome_bam, genome_star_bam]
to_delete = [without_rrna]
out_files = [genome_star_bam]
file_checkers = {
#transcriptome_bam: bam_utils.check_bam_file,
genome_star_bam: bam_utils.check_bam_file
}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call,
keep_delete_files=keep_delete_files,
to_delete=to_delete)
# now, we need to symlink the (genome) STAR output to that expected by the rest of the pipeline
genome_sorted_bam = filenames.get_riboseq_bam(config['riboseq_data'],
args.name,
note=note)
if os.path.exists(genome_star_bam):
utils.create_symlink(genome_star_bam, genome_sorted_bam, call)
else:
msg = ("Could not find the STAR genome bam alignment file. Unless "
"--do-not-call was given, this is a problem.")
logger.warning(msg)
# create the bamtools index
cmd = "samtools index -b {}".format(genome_sorted_bam)
shell_utils.check_call(cmd, call=call)
# check if we want to keep multimappers
if 'keep_riboseq_multimappers' in config:
return
# remove multimapping reads from the genome file
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
unique_genome_filename = filenames.get_riboseq_bam(config['riboseq_data'],
args.name,
is_unique=True,
note=note)
cmd = "remove-multimapping-reads {} {} {}".format(genome_sorted_bam,
unique_genome_filename,
tmp_str)
in_files = [genome_sorted_bam]
out_files = [unique_genome_filename]
to_delete = [genome_star_bam, genome_sorted_bam]
file_checkers = {unique_genome_filename: bam_utils.check_bam_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call,
keep_delete_files=keep_delete_files,
to_delete=to_delete)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script runs the second part of the pipeline: it estimate ORF Bayes"
"factors using the ORF profiles, then make the final prediction set.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('name', help="The name for the dataset, used in the created files")
parser.add_argument('-p', '--num-cpus', help="The number of processors to use",
type=int, default=default_num_cpus)
parser.add_argument('--do-not-call', action='store_true')
parser.add_argument('--overwrite', help="If this flag is present, existing files "
"will be overwritten.", action='store_true')
parser.add_argument('--merge-replicates', help="If this flag is present, then the ORF "
"profiles will be merged for all replicates in the condition given by <name>. The "
"filenames, etc., will reflect the condition name, but not the lengths and offsets "
"of the individual replicates.\n\nN.B. If this flag is is present, the --overwrite "
"flag will automatically be set!", action='store_true')
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
msg = "[predict_translated_orfs]: {}".format(' '.join(sys.argv))
logger.debug(msg)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'estimate-orf-bayes-factors',
'select-final-prediction-set'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data',
'fasta',
'genome_base_path',
'genome_name'
]
utils.check_keys_exist(config, required_keys)
models_base = config.get('models_base', default_models_base)
note_str = config.get('note', None)
# we always need the ORFs
orfs_genomic = filenames.get_orfs(
config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note')
)
# smoothing parameters (filenames)
# default values are not used in the file names
fraction = config.get('smoothing_fraction', None)
reweighting_iterations = config.get('smoothing_reweighting_iterations', None)
# check if we are running Rp-Bp (default) or Rp-chi
chi_square_only_str = ""
chi_square_only = False
if 'chi_square_only' in config:
chi_square_only_str = "--chi-square-only"
chi_square_only = True
fraction = None
reweighting_iterations = None
msg = """ The final prediction set will be made based on the chi square test only!
The translation models will not be fit to the data, and the posterior
distributions will not be estimated. """
logger.info(msg)
# keep multimappers?
is_unique = not ('keep_riboseq_multimappers' in config)
# first, check if we are merging replicates
# either way, the following variables need to have values for the rest of
# the pipeline: lengths, offsets, smooth_profiles
if args.merge_replicates:
msg = ("The --merge-replicates option was given, so --overwrite is "
"being set to True.")
logger.warning(msg)
args.overwrite = True
# now, actually merge the replicates
riboseq_replicates = ribo_utils.get_riboseq_replicates(config)
# we will not use the lengths and offsets in the filenames
lengths = None
offsets = None
# we will also merge all of unsmoothed profiles
replicate_profiles = [
get_profile(name, config, args)
for name in riboseq_replicates[args.name]
]
replicate_profiles_str = ' '.join(replicate_profiles)
profiles = filenames.get_riboseq_profiles(config['riboseq_data'], args.name,
length=lengths, offset=offsets, is_unique=is_unique, note=note_str)
cmd = "merge-replicate-orf-profiles {} {} {}".format(replicate_profiles_str,
profiles, logging_str)
in_files = replicate_profiles
out_files = [profiles]
# todo: implement file checker for mtx files
shell_utils.call_if_not_exists(
cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=call
)
else:
# otherwise, just treat things as normal
# get the lengths and offsets which meet the required criteria from
# the config file
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(config,
args.name, args.do_not_call, is_unique=is_unique)
profiles = get_profile(args.name, config, args)
# estimate the bayes factors
bayes_factors = filenames.get_riboseq_bayes_factors(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations
)
# the smoothing options
min_length_str = utils.get_config_argument(config, 'min_orf_length', 'min-length')
max_length_str = utils.get_config_argument(config, 'max_orf_length', 'max-length')
min_profile_str = utils.get_config_argument(config, 'min_signal', 'min-profile')
fraction_str = utils.get_config_argument(config, 'smoothing_fraction', 'fraction')
reweighting_iterations_str = utils.get_config_argument(config,
'smoothing_reweighting_iterations', 'reweighting-iterations')
# parse out all of the options from the config file, if they are present
translated_models = filenames.get_models(models_base, 'translated')
untranslated_models = filenames.get_models(models_base, 'untranslated')
translated_models_str = ' '.join(translated_models)
untranslated_models_str = ' '.join(untranslated_models)
translated_models_str = "--translated-models {}".format(
translated_models_str)
untranslated_models_str = "--untranslated-models {}".format(
untranslated_models_str)
orf_types_str = utils.get_config_argument(config, 'orf_types')
seed_str = utils.get_config_argument(config, 'seed')
chains_str = utils.get_config_argument(config, 'chains', 'chains')
iterations_str = utils.get_config_argument(config, 'translation_iterations', 'iterations')
cmd = ("estimate-orf-bayes-factors {} {} {} {} {} {} {} {} {} {} {} {} {} {} {} {} "
"--num-cpus {}".format(
profiles,
orfs_genomic,
bayes_factors,
translated_models_str,
untranslated_models_str,
logging_str,
orf_types_str,
min_length_str,
max_length_str,
min_profile_str,
fraction_str,
reweighting_iterations_str,
seed_str,
iterations_str,
chains_str,
chi_square_only_str,
args.num_cpus)
)
in_files = [profiles, orfs_genomic]
in_files.extend(translated_models)
in_files.extend(untranslated_models)
out_files = [bayes_factors]
file_checkers = {
bayes_factors: utils.check_gzip_file
}
msg = "estimate-bayes-factors in_files: {}".format(in_files)
logger.debug(msg)
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
file_checkers=file_checkers, overwrite=args.overwrite, call=call)
for is_filtered in [True, False]:
filtered_str = ""
if is_filtered:
filtered_str = "--select-longest-by-stop --select-best-overlapping"
# now, select the ORFs (longest for each stop codon) which pass the prediction filters
predicted_orfs = filenames.get_riboseq_predicted_orfs(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=chi_square_only
)
predicted_orfs_dna = filenames.get_riboseq_predicted_orfs_dna(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=chi_square_only
)
predicted_orfs_protein = filenames.get_riboseq_predicted_orfs_protein(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=chi_square_only
)
min_bf_mean_str = utils.get_config_argument(config, 'min_bf_mean')
max_bf_var_str = utils.get_config_argument(config, 'max_bf_var')
min_bf_likelihood_str = utils.get_config_argument(config, 'min_bf_likelihood')
chisq_significance_level_str = utils.get_config_argument(config, 'chisq_significance_level')
min_profile_str = utils.get_config_argument(config, 'min_signal', 'minimum-profile-sum')
cmd = "select-final-prediction-set {} {} {} {} {} {} {} {} {} {} {}".format(
bayes_factors,
config['fasta'],
predicted_orfs,
predicted_orfs_dna,
predicted_orfs_protein,
min_bf_mean_str,
max_bf_var_str,
min_bf_likelihood_str,
logging_str,
chi_square_only_str,
filtered_str
)
in_files = [bayes_factors, config['fasta']]
out_files = [
predicted_orfs,
predicted_orfs_dna,
predicted_orfs_protein
]
file_checkers = {
predicted_orfs: utils.check_gzip_file
}
# todo: implement file checker for fasta files
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
file_checkers=file_checkers, overwrite=args.overwrite, call=call)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script creates the plots which detail the basic characteristics "
"of the ORF predictions from the Rp-Bp pipeline. It also creates and compiles (if "
"possible) a latex report for them.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('out',
help="The base output directory for the latex report")
parser.add_argument(
'--show-unfiltered-orfs',
help="If this flag is "
"present, bar charts showing the distribution of the types of the "
"unfiltered ORF set will be included",
action='store_true')
parser.add_argument(
'--show-orf-periodicity',
help="If this flag is "
"present, bar charts showing the periodicity of each ORF type will be "
"included in the report.",
action='store_true')
parser.add_argument('--uniprot',
help="The uniprot ORF lengths, if available",
default=default_uniprot)
parser.add_argument('--uniprot-label',
help="The label to use for the uniprot ORFs in "
"the plot",
default=default_uniprot_label)
parser.add_argument('--image-type',
help="The format of the image files. This must be "
"a format usable by matplotlib.",
default=default_image_type)
parser.add_argument('--overwrite',
help="If this flag is present, existing files will "
"be overwritten.",
action='store_true')
parser.add_argument(
'--note',
help="If this option is given, it will be used in the "
"filenames.\n\nN.B. This REPLACES the note in the config file.",
default=default_note)
parser.add_argument(
'--show-chisq',
help="If this flag is given, then the "
"results from Rp-chi will be included in the document; otherwise, they "
"will not be created or shown.",
action='store_true')
parser.add_argument('-t',
'--tmp',
help="A location for temporary files",
default=default_tmp)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
config = yaml.load(open(args.config))
# keep multimappers?
is_unique = not ('keep_riboseq_multimappers' in config)
programs = [
'create-orf-length-distribution-line-graph',
'create-orf-types-bar-chart', 'visualize-orf-type-metagene-profiles'
]
shell_utils.check_programs_exist(programs)
required_keys = ['riboseq_data', 'riboseq_samples']
utils.check_keys_exist(config, required_keys)
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
# by default, we will not include chisq
chisq_values = [False]
if args.show_chisq:
chisq_values = [True, False]
filtered_values = [True]
if args.show_unfiltered_orfs:
filtered_values = [True, False]
grouped_values = [True, False]
# make sure the path to the output file exists
os.makedirs(args.out, exist_ok=True)
# first, create all of the figures
create_all_figures(config, args)
note_str = config.get('note', None)
out_note_str = note_str
if args.note is not None and len(args.note) > 0:
out_note_str = args.note
fraction = config.get('smoothing_fraction', None)
reweighting_iterations = config.get('smoothing_reweighting_iterations',
None)
project_name = config.get("project_name", default_project_name)
title = "Rp-Bp prediction analysis for {}".format(project_name)
abstract = "This document shows the results of the Rp-Bp pipeline analysis."
#tex_file = os.path.join(args.out, "prediction-report.tex")
tex_file = filenames.get_rpbp_prediction_report(args.out, out_note_str)
with open(tex_file, 'w') as out:
latex.begin_document(out, title, abstract)
latex.write(out, "\n")
latex.clearpage(out)
### ORF type distributions
title = "Predicted ORF type distributions"
latex.section(out, title)
# first, handle all of the regular datasets
sample_names = sorted(config['riboseq_samples'].keys())
# and check if we also have replicates
replicate_names = []
if 'riboseq_biological_replicates' in config:
replicate_names = sorted(
ribo_utils.get_riboseq_replicates(config).keys())
strands = ["+", "-"]
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = (
"Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF types: {}".format(sample_name)
is_first = True
# first, just dump all of the bar charts to the page
it = itertools.product(grouped_values, chisq_values,
filtered_values)
for is_grouped, is_chisq, is_filtered in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_types_bar_chart = filenames.get_orf_types_bar_chart(
config['riboseq_data'],
sample_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq,
is_filtered=is_filtered)
msg = "Looking for image file: {}".format(orf_types_bar_chart)
logger.debug(msg)
if os.path.exists(orf_types_bar_chart):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_types_bar_chart, height=0.15)
if i % 6 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_types_bar_chart)
logger.warning(msg)
if (i > 0) and (i % 6) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 6 != 0:
latex.clearpage(out)
# now, if the config file specifies replicates, create figures for those
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF types: {}".format(replicate_name)
it = itertools.product(grouped_values, chisq_values,
filtered_values)
is_first = True
for is_grouped, is_chisq, is_filtered in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_types_bar_chart = filenames.get_orf_types_bar_chart(
config['riboseq_data'],
replicate_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq,
is_filtered=is_filtered)
msg = "Looking for image file: {}".format(orf_types_bar_chart)
logger.debug(msg)
if os.path.exists(orf_types_bar_chart):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out, orf_types_bar_chart, height=0.15)
if i % 6 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_types_bar_chart)
logger.warning(msg)
if (i > 0) and (i % 6) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 6 != 0:
latex.clearpage(out)
### ORF type length distributions
title = "Predicted ORF type length distributions"
latex.section(out, title)
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = (
"Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF type length distributions: {}".format(sample_name)
is_first = True
it = itertools.product(grouped_values, chisq_values)
for is_grouped, is_chisq in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_length_line_graph = filenames.get_orf_length_distribution_line_graph(
config['riboseq_data'],
sample_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq)
if os.path.exists(orf_length_line_graph):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out,
orf_length_line_graph,
height=0.15)
if i % 4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_length_line_graph)
logger.debug(msg)
if (i > 0) and (i % 4) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 4 != 0:
latex.clearpage(out)
# now, if the config file specifies replicates, create figures for those
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF types: {}".format(replicate_name)
is_first = True
it = itertools.product(grouped_values, chisq_values)
for is_grouped, is_chisq in it:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_length_line_graph = filenames.get_orf_length_distribution_line_graph(
config['riboseq_data'],
replicate_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
image_type=args.image_type,
fraction=f,
reweighting_iterations=rw,
is_grouped=is_grouped,
is_chisq=is_chisq)
if os.path.exists(orf_length_line_graph):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out,
orf_length_line_graph,
height=0.15)
if i % 4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_length_line_graph)
logger.debug(msg)
if (i > 0) and (i % 4) != 0:
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 4 != 0:
latex.clearpage(out)
### ORF type metagene profiles
if args.show_orf_periodicity:
title = "Predicted ORF type metagene profiles"
latex.section(out, title)
i = 0
for sample_name in sample_names:
try:
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, sample_name, is_unique=is_unique)
except FileNotFoundError:
msg = (
"Could not parse out lengths and offsets for sample: {}. "
"Skipping".format(sample_name))
logger.error(msg)
continue
caption = "ORF type metagene profiles: {}".format(sample_name)
is_first = True
for is_chisq in chisq_values:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_type_profile_base = filenames.get_orf_type_profile_base(
config['riboseq_data'],
sample_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
fraction=f,
reweighting_iterations=rw,
is_chisq=is_chisq)
it = itertools.product(ribo_utils.orf_types, strands)
for orf_type, strand in it:
orf_type_profile = filenames.get_orf_type_profile_image(
orf_type_profile_base, orf_type, strand,
args.image_type)
msg = "Looking for image file: {}".format(
orf_type_profile)
logger.debug(msg)
if os.path.exists(orf_type_profile):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out,
orf_type_profile,
height=0.23)
if i % 4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_type_profile)
logger.warning(msg)
if (i > 0) and (i % 4 != 0):
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 4 != 0:
latex.clearpage(out)
i = 0
for replicate_name in replicate_names:
lengths = None
offsets = None
caption = "ORF type metagene profiles: {}".format(
replicate_name)
is_first = True
for is_chisq in chisq_values:
if is_chisq:
f = None
rw = None
else:
f = fraction
rw = reweighting_iterations
orf_type_profile_base = filenames.get_orf_type_profile_base(
config['riboseq_data'],
replicate_name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=out_note_str,
fraction=f,
reweighting_iterations=rw,
is_chisq=is_chisq)
it = itertools.product(ribo_utils.orf_types, strands)
for orf_type, strand in it:
orf_type_profile = filenames.get_orf_type_profile_image(
orf_type_profile_base, orf_type, strand,
args.image_type)
if os.path.exists(orf_type_profile):
if is_first or (i % 4 == 0):
latex.begin_figure(out)
is_first = False
i += 1
latex.write_graphics(out,
orf_type_profile,
height=0.23)
if i % 4 == 0:
latex.write_caption(out, caption)
latex.end_figure(out)
latex.clearpage(out)
else:
msg = "Could not find image: {}".format(
orf_type_profile)
logger.debug(msg)
if (i > 0) and (i % 4 != 0):
latex.write_caption(out, caption)
latex.end_figure(out)
#latex.clearpage(out)
if i % 4 != 0:
latex.clearpage(out)
latex.end_document(out)
tex_filename = os.path.basename(tex_file)
latex.compile(args.out, tex_filename)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script runs the Rp-Bp and Rp-chi pipelines on a given sample. "
"It requires a YAML config file that includes a number of keys. Please see the "
"documentation for a complete description.")
parser.add_argument('raw_data', help="The raw data file (fastq[.gz])")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument(
'name', help="The name for the dataset, used in the created files")
parser.add_argument('--tmp',
help="The temp directory",
default=default_tmp)
parser.add_argument(
'--flexbar-format-option',
help="The name of the \"format\" "
"option for flexbar. This changed from \"format\" to \"qtrim-format\" in "
"version 2.7.",
default=default_flexbar_format_option)
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
parser.add_argument('--profiles-only',
help="If this flag is present, then only "
"the ORF profiles will be created",
action='store_true')
parser.add_argument(
'-k',
'--keep-intermediate-files',
help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.",
action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar', args.star_executable, 'samtools', 'bowtie2',
'create-base-genome-profile', 'remove-multimapping-reads',
'extract-metagene-profiles', 'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets', 'extract-orf-profiles',
'estimate-orf-bayes-factors', 'select-final-prediction-set',
'create-orf-profiles', 'predict-translated-orfs'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data', 'ribosomal_index', 'star_index', 'genome_base_path',
'genome_name', 'fasta', 'gtf'
]
utils.check_keys_exist(config, required_keys)
# now, check if we want to use slurm
msg = "use_slurm: {}".format(args.use_slurm)
logger.debug(msg)
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
note_str = config.get('note', None)
# the first step is the standard riboseq preprocessing
# handle do_not_call so that we _do_ call the preprocessing script,
# but that it does not run anything
do_not_call_str = ""
if not call:
do_not_call_str = "--do-not-call"
overwrite_str = ""
if args.overwrite:
overwrite_str = "--overwrite"
# for a sample, we first create its filtered genome profile
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_format_option_str = ""
if args.flexbar_format_option is not None:
flexbar_format_option_str = "--flexbar-format-option {}".format(
args.flexbar_format_option)
mem_str = "--mem {}".format(shlex.quote(args.mem))
cmd = ("create-orf-profiles {} {} {} --num-cpus {} {} {} {} {} {} {} {} {}"
.format(args.raw_data, args.config, args.name, args.num_cpus,
mem_str, do_not_call_str, overwrite_str, logging_str,
star_str, tmp_str, flexbar_format_option_str,
keep_intermediate_str))
shell_utils.check_call(cmd)
# check if we only want to create the profiles
if args.profiles_only:
return
# then we predict the ORFs
cmd = ("predict-translated-orfs {} {} --num-cpus {} {} {} {}".format(
args.config, args.name, args.num_cpus, do_not_call_str, overwrite_str,
logging_str))
shell_utils.check_call(cmd)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script creates a simple latex document.")
parser.add_argument('config', help="The (yaml) config file for the project")
parser.add_argument('out', help="The path for the output files")
parser.add_argument('-l', '--min-orf-length', help="The minimum length for ORFs (in "
"nucleotides) to consider in the analyis", type=int, default=default_min_orf_length)
parser.add_argument('--num-cpus', help="The number of processors to use for counting "
"the matching peptides coverage for each predicted ORF.",
type=int, default=default_num_cpus)
parser.add_argument('--overwrite', help="If this flag is present, existing files will "
"be overwritten.", action='store_true')
parser.add_argument('--note', help="If this option is given, it will be used in the "
"filenames.\n\nN.B. This REPLACES the note in the config file.", default=default_note)
utils.add_logging_options(parser)
args = parser.parse_args()
utils.update_logging(args)
config = yaml.load(open(args.config))
# keep multimappers?
is_unique = not ('keep_riboseq_multimappers' in config)
programs = [
'create-orf-peptide-coverage-line-graph'
]
utils.check_programs_exist(programs)
required_keys = [
'riboseq_data',
'riboseq_samples'
]
utils.check_keys_exist(config, required_keys)
# make sure the path to the output file exists
os.makedirs(args.out, exist_ok=True)
note_str = config.get('note', None)
out_note_str = note_str
if args.note is not None and len(args.note) > 0:
out_note_str = args.note
project_name = config.get("project_name", default_project_name)
title = "Proteomics analysis for {}".format(project_name)
abstract = "This document shows the results of proteomics analysis."
header = latex.get_header_text(title, abstract)
footer = latex.get_footer_text()
tex_file = os.path.join(args.out, "proteomics-report.tex")
with open(tex_file, 'w') as out:
out.write(header)
out.write("\n")
title = "ORF peptide coverage"
latex.section(out, title)
for name, data in config['riboseq_samples'].items():
msg = "Processing sample: {}".format(name)
logging.info(msg)
logging.debug("overwrite: {}".format(args.overwrite))
create_figures(args.config, config, name, args)
title = name
latex.subsection(out, title)
try:
lengths, offsets = riboutils.ribo_utils.get_periodic_lengths_and_offsets(
config, name, is_unique=is_unique)
except FileNotFoundError:
msg = "Could not parse out lengths and offsets for sample: {}. Skipping".format(name)
logging.error(msg)
return
peptide_coverage_line_graph = filenames.get_peptide_coverage_line_graph(config['riboseq_data'],
name, length=lengths, offset=offsets, is_unique=is_unique, note=out_note_str)
if os.path.exists(peptide_coverage_line_graph):
latex.begin_figure(out)
latex.write_graphics(out, peptide_coverage_line_graph, width=0.9)
latex.end_figure(out)
else:
text = "Problem creating ORF peptide coverage plot"
out.write(text)
out.write("\n")
latex.clearpage(out)
out.write(footer)
os.chdir(args.out)
cmd = "pdflatex -shell-escape proteomics-report"
utils.check_call(cmd)
utils.check_call(cmd) # call again to fix references
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script identifies the orf peptide matches for all samples in "
"a project.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--peptide-filter-field', help="The field to use for "
"filtering the peptides from MaxQuant", default=default_peptide_filter_field)
parser.add_argument('--peptide-filter-value', help="All peptides with a value "
"greater than the filter value will be removed", type=float,
default=default_peptide_filter_value)
parser.add_argument('--peptide-separator', help="The separator in the "
"peptide file", default=default_peptide_separator)
parser.add_argument('--note', help="If this option is given, it will be used in "
"the output filenames.\n\nN.B. This REPLACES the note in the config file.",
default=default_note)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
programs = [
'get-orf-peptide-matches'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'peptide_files',
'peptide_cell_type_analysis',
'riboseq_data',
'riboseq_samples'
]
utils.check_keys_exist(config, required_keys)
note_str = config.get('note', None)
out_note_str = note_str
if args.note is not None and len(args.note) > 0:
out_note_str = args.note
args_dict = vars(args)
peptide_filter_field_str = utils.get_config_argument(args_dict, 'peptides_filter_field')
peptide_filter_value_str = utils.get_config_argument(args_dict, 'peptides_filter_value')
peptide_separator_str = utils.get_config_argument(args_dict, 'peptide_separator')
num_cpus_str = utils.get_config_argument(args_dict, 'num_cpus')
cell_types = ribo_utils.get_riboseq_cell_type_samples(config)
for cell_type, peptide_files in config['peptide_cell_type_analysis'].items():
if cell_type not in cell_types:
msg = ("Could not find cell_type specification. Please check the config "
"file: {}".format(cell_type))
logger.warning(msg)
continue
cell_type_protein = ribo_filenames.get_riboseq_cell_type_protein(
config['riboseq_data'], cell_type, is_filtered=True, note=note_str)
if not os.path.exists(cell_type_protein):
msg = ("Could not find cell_type protein fasta. Skipping: {}".
format(cell_type_protein))
logger.warning(msg)
continue
for peptide_file in peptide_files:
if peptide_file not in config['peptide_files']:
msg = ("Could not find peptide_file specification. Please check "
"the config file: {}".format(peptide_file))
logger.warning(msg)
continue
peptide_txt_file = config['peptide_files'][peptide_file]
if not os.path.exists(peptide_txt_file):
msg = ("Could not find peptide.txt file. Skipping: {}".
format(peptide_txt_file))
logger.warning(msg)
continue
peptide_matches = ribo_filenames.get_riboseq_peptide_matches(
config['riboseq_data'], cell_type, peptide_file,
is_filtered=True, note=out_note_str)
cmd = "get-orf-peptide-matches {} {} {} {} {} {} {} {}".format(cell_type_protein,
peptide_txt_file, peptide_matches, num_cpus_str, peptide_filter_field_str,
peptide_filter_value_str, peptide_separator_str, logging_str)
slurm.check_sbatch(cmd, args=args)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script identifies the orf peptide matches for all samples in "
"a project.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--peptide-filter-field',
help="The field to use for "
"filtering the peptides from MaxQuant",
default=default_peptide_filter_field)
parser.add_argument('--peptide-filter-value',
help="All peptides with a value "
"greater than the filter value will be removed",
type=float,
default=default_peptide_filter_value)
parser.add_argument('--peptide-separator',
help="The separator in the "
"peptide file",
default=default_peptide_separator)
parser.add_argument(
'--note',
help="If this option is given, it will be used in "
"the output filenames.\n\nN.B. This REPLACES the note in the config file.",
default=default_note)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
programs = ['get-orf-peptide-matches']
shell_utils.check_programs_exist(programs)
required_keys = [
'peptide_files', 'peptide_cell_type_analysis', 'riboseq_data',
'riboseq_samples'
]
utils.check_keys_exist(config, required_keys)
note_str = config.get('note', None)
out_note_str = note_str
if args.note is not None and len(args.note) > 0:
out_note_str = args.note
args_dict = vars(args)
peptide_filter_field_str = utils.get_config_argument(
args_dict, 'peptides_filter_field')
peptide_filter_value_str = utils.get_config_argument(
args_dict, 'peptides_filter_value')
peptide_separator_str = utils.get_config_argument(args_dict,
'peptide_separator')
num_cpus_str = utils.get_config_argument(args_dict, 'num_cpus')
cell_types = ribo_utils.get_riboseq_cell_type_samples(config)
for cell_type, peptide_files in config['peptide_cell_type_analysis'].items(
):
if cell_type not in cell_types:
msg = (
"Could not find cell_type specification. Please check the config "
"file: {}".format(cell_type))
logger.warning(msg)
continue
cell_type_protein = ribo_filenames.get_riboseq_cell_type_protein(
config['riboseq_data'], cell_type, is_filtered=True, note=note_str)
if not os.path.exists(cell_type_protein):
msg = ("Could not find cell_type protein fasta. Skipping: {}".
format(cell_type_protein))
logger.warning(msg)
continue
for peptide_file in peptide_files:
if peptide_file not in config['peptide_files']:
msg = (
"Could not find peptide_file specification. Please check "
"the config file: {}".format(peptide_file))
logger.warning(msg)
continue
peptide_txt_file = config['peptide_files'][peptide_file]
if not os.path.exists(peptide_txt_file):
msg = ("Could not find peptide.txt file. Skipping: {}".format(
peptide_txt_file))
logger.warning(msg)
continue
peptide_matches = ribo_filenames.get_riboseq_peptide_matches(
config['riboseq_data'],
cell_type,
peptide_file,
is_filtered=True,
note=out_note_str)
cmd = "get-orf-peptide-matches {} {} {} {} {} {} {} {}".format(
cell_type_protein, peptide_txt_file, peptide_matches,
num_cpus_str, peptide_filter_field_str,
peptide_filter_value_str, peptide_separator_str, logging_str)
slurm.check_sbatch(cmd, args=args)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script creates all of the files necessary for downstream "
"analysis performed with the rpbp package.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'extract-orf-coordinates', 'label-orfs', 'bowtie2-build-s',
'split-bed12-blocks', 'gtf-to-bed12', args.star_executable
]
shell_utils.check_programs_exist(programs)
required_keys = [
'genome_base_path', 'genome_name', 'gtf', 'fasta', 'ribosomal_fasta',
'ribosomal_index', 'star_index'
]
utils.check_keys_exist(config, required_keys)
# check that the required files are present
files = [config['gtf'], config['fasta'], config['ribosomal_fasta']]
if 'de_novo_gtf' in config:
files += [config['de_novo_gtf']]
utils.check_files_exist(files, source='prepare-rpbp-genome')
# now, check if we want to use slurm
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
# the rrna index
cmd = "bowtie2-build-s {} {}".format(config['ribosomal_fasta'],
config['ribosomal_index'])
in_files = [config['ribosomal_fasta']]
out_files = bio.get_bowtie2_index_files(config['ribosomal_index'])
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=call)
# the STAR index
mem = utils.human2bytes(args.mem)
cmd = ("{} --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} "
"--runThreadN {} --limitGenomeGenerateRAM {}".format(
args.star_executable, config['star_index'], config['fasta'],
args.num_cpus, mem))
in_files = [config['fasta']]
out_files = star_utils.get_star_index_files(config['star_index'])
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=call)
# get the main orfs
get_orfs(config['gtf'], args, config, is_annotated=True, is_de_novo=False)
# eventually, we will use these names
annotated_orfs = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'),
is_annotated=True,
is_de_novo=False)
annotated_exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'),
is_annotated=True,
is_de_novo=False)
orfs_genomic = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
# now, check if we have a de novo assembly
if 'de_novo_gtf' in config:
get_orfs(config['de_novo_gtf'],
args,
config,
is_annotated=False,
is_de_novo=True)
# we need to concat the ORF and exon files
de_novo_orfs = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'),
is_annotated=False,
is_de_novo=True)
de_novo_exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'),
is_annotated=False,
is_de_novo=True)
orfs_files = [annotated_orfs, de_novo_orfs]
orfs_files_str = ' '.join(orfs_files)
msg = ("Concatenating files. Output file: {}; Input files: {}".format(
orfs_genomic, orfs_files_str))
logger.info(msg)
if call:
concatenated_bed = bed_utils.concatenate(orfs_files, sort_bed=True)
concatenated_bed['orf_num'] = range(len(concatenated_bed))
fields = bed_utils.bed12_field_names + [
'orf_num', 'orf_len', 'orf_type'
]
bed_utils.write_bed(concatenated_bed[fields], orfs_genomic)
else:
msg = "Skipping concatenation due to --call value"
logger.info(msg)
exons_files = [annotated_exons_file, de_novo_exons_file]
exons_files_str = ' '.join(exons_files)
msg = ("Concatenating files. Output file: {}; Input files: {}".format(
exons_file, exons_files_str))
logger.info(msg)
if call:
concatenated_bed = bed_utils.concatenate(exons_files,
sort_bed=True)
fields = bed_utils.bed6_field_names + [
'exon_index', 'transcript_start'
]
bed_utils.write_bed(concatenated_bed[fields], exons_file)
else:
msg = "Skipping concatenation due to --call value"
logger.info(msg)
else:
# finally, make sure our files are named correctly
if os.path.exists(annotated_orfs):
utils.create_symlink(annotated_orfs, orfs_genomic, call)
if os.path.exists(annotated_exons_file):
utils.create_symlink(annotated_exons_file, exons_file, call)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This is a helper script which submits a set of samples to SLURM. It "
"can also be used to run a set of samples sequentially. Due to limitations on "
"the config file specification, all of the samples must use the same reference "
"indices (i.e., genome sequence, set of ORFs, etc.).")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--tmp', help="The temp directory", default=default_tmp)
parser.add_argument('--flexbar-options', help="A space-delimited list of options to"
"pass to flexbar. Each option must be quoted separately as in \"--flexbarOption value\""
"If specified, flexbar options will override default settings.", nargs='*', type=str)
parser.add_argument('--overwrite', help="If this flag is present, existing files "
"will be overwritten.", action='store_true')
parser.add_argument('--profiles-only', help="If this flag is present, then only "
"the pre-processing part of the pipeline will be called, i.e. profiles "
"will be created for each sample specified in the config file, but no predictions"
"will be made.", action='store_true')
parser.add_argument('--merge-replicates', help="If this flag is present, then "
"the ORF profiles from the replicates will be merged before making the final "
"predictions", action='store_true')
parser.add_argument('--run-replicates', help="If this flag is given with the "
"--merge-replicates flag, then both the replicates *and* the individual "
"samples will be run. This flag has no effect if --merge-replicates is not "
"given.", action='store_true')
parser.add_argument('-k', '--keep-intermediate-files', help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.", action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar',
args.star_executable,
'samtools',
'bowtie2',
'create-base-genome-profile',
'remove-multimapping-reads',
'extract-metagene-profiles',
'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets',
'extract-orf-profiles',
'estimate-orf-bayes-factors',
'select-final-prediction-set',
'create-orf-profiles',
'predict-translated-orfs',
'run-rpbp-pipeline'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data',
'riboseq_samples',
'ribosomal_index',
'star_index',
'genome_base_path',
'genome_name',
'fasta',
'gtf'
]
utils.check_keys_exist(config, required_keys)
note = config.get('note', None)
# handle do_not_call so that we _do_ call the pipeline script, but that it does not run anything
do_not_call_str = ""
if not call:
do_not_call_str = "--do-not-call"
args.do_not_call = False
overwrite_str = ""
if args.overwrite:
overwrite_str = "--overwrite"
mem_str = "--mem {}".format(shlex.quote(args.mem))
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
# check if we only want to create the profiles, in this case
# we call run-rpbp-pipeline with the --profiles-only option
profiles_only_str = ""
if args.profiles_only:
args.merge_replicates = False
profiles_only_str = "--profiles-only"
msg = ("The --profiles-only option was given, this will override --merge-replicates "
"and/or --run-replicates, if these options were also given!")
logger.info(msg)
# if we merge the replicates, then we only use the rpbp script to create
# the ORF profiles, but we still make predictions
if args.merge_replicates and not args.run_replicates:
profiles_only_str = "--profiles-only"
if args.run_replicates and not args.merge_replicates:
msg = ("The --run-replicates option was given without the --merge-replicates "
"option. It will be ignored.")
logger.warning(msg)
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_option_str = ""
if args.flexbar_options is not None:
flexbar_option_str = "--flexbar-options {}".format(' '.join('"' + flx_op + '"'
for flx_op in args.flexbar_options))
# collect the job_ids in case we are using slurm and need to merge replicates
job_ids = []
sample_names = sorted(config['riboseq_samples'].keys())
for sample_name in sample_names:
data = config['riboseq_samples'][sample_name]
tmp_str = ""
if args.tmp is not None:
tmp = os.path.join(args.tmp, "{}_{}_rpbp".format(sample_name, note))
tmp_str = "--tmp {}".format(tmp)
cmd = "run-rpbp-pipeline {} {} {} --num-cpus {} {} {} {} {} {} {} {} {} {}".format(
data,
args.config,
sample_name,
args.num_cpus,
tmp_str,
do_not_call_str,
overwrite_str,
logging_str,
star_str,
profiles_only_str,
flexbar_option_str,
keep_intermediate_str,
mem_str
)
job_id = slurm.check_sbatch(cmd, args=args)
job_ids.append(job_id)
# now, if we are running the "standard" pipeline, we are finished
if not args.merge_replicates:
return
# otherwise, we need to merge the replicates for each condition
riboseq_replicates = ribo_utils.get_riboseq_replicates(config)
merge_replicates_str = "--merge-replicates"
for condition_name in sorted(riboseq_replicates.keys()):
# then we predict the ORFs
cmd = "predict-translated-orfs {} {} --num-cpus {} {} {} {} {}".format(
args.config,
condition_name,
args.num_cpus,
do_not_call_str,
overwrite_str,
logging_str,
merge_replicates_str
)
slurm.check_sbatch(cmd, args=args, dependencies=job_ids)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script runs all of the processing necessary to produce the "
"signals used for later processing. In particular, it runs the standard "
"rnaseq and riboseq preprocessing, estimates the abundance of transcripts with "
"the rnaseq data, and selects the most-expressed isoforms and ORFs. Next, it removes "
"multimapping and non-periodic-length riboseq reads. Finally, it extracts the riboseq "
"signal for the most-expressed transcripts.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument(
'name', help="The name for the dataset, used in the created files")
parser.add_argument('-p',
'--num-cpus',
help="The number of processors to use",
type=int,
default=default_num_cpus)
parser.add_argument('--do-not-call', action='store_true')
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
parser.add_argument(
'--merge-replicates',
help="If this flag is present, then the ORF "
"profiles will be merged for all replicates in the condition given by <name>. The "
"filenames, etc., will reflect the condition name, but not the lengths and offsets "
"of the individual replicates.\n\nN.B. If this flag is is present, the --overwrite "
"flag will automatically be set!",
action='store_true')
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
msg = "[predict_translated_orfs]: {}".format(' '.join(sys.argv))
logger.debug(msg)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = ['estimate-orf-bayes-factors', 'select-final-prediction-set']
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data', 'fasta', 'genome_base_path', 'genome_name'
]
utils.check_keys_exist(config, required_keys)
models_base = config.get('models_base', default_models_base)
note_str = config.get('note', None)
# we always need the ORFs
orfs_genomic = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
# and the smoothing parameters
fraction = config.get('smoothing_fraction', None)
reweighting_iterations = config.get('smoothing_reweighting_iterations',
None)
# keep multimappers?
is_unique = not ('keep_riboseq_multimappers' in config)
# first, check if we are merging replicates
# either way, the following variables need to have values for the rest of
# the pipeline: lengths, offsets, smooth_profiles
if args.merge_replicates:
msg = ("The --merge-replicates option was given, so --overwrite is "
"being set to True.")
logger.warning(msg)
args.overwrite = True
# now, actually merge the replicates
riboseq_replicates = ribo_utils.get_riboseq_replicates(config)
# we will not use the lengths and offsets in the filenames
lengths = None
offsets = None
# we will also merge all of unsmoothed profiles
replicate_profiles = [
get_profile(name, config, args)
for name in riboseq_replicates[args.name]
]
replicate_profiles_str = ' '.join(replicate_profiles)
profiles = filenames.get_riboseq_profiles(config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str)
cmd = "merge-replicate-orf-profiles {} {} {}".format(
replicate_profiles_str, profiles, logging_str)
in_files = replicate_profiles
out_files = [profiles]
# todo: implement file checker for mtx files
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=call)
else:
# otherwise, just treat things as normal
# get the lengths and offsets which meet the required criteria from
# the config file
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, args.name, args.do_not_call, is_unique=is_unique)
profiles = get_profile(args.name, config, args)
# estimate the bayes factors
bayes_factors = filenames.get_riboseq_bayes_factors(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations)
# the smoothing options
min_length_str = utils.get_config_argument(config, 'min_orf_length',
'min-length')
max_length_str = utils.get_config_argument(config, 'max_orf_length',
'max-length')
min_profile_str = utils.get_config_argument(config, 'min_signal',
'min-profile')
fraction_str = utils.get_config_argument(config, 'smoothing_fraction',
'fraction')
reweighting_iterations_str = utils.get_config_argument(
config, 'smoothing_reweighting_iterations', 'reweighting-iterations')
# parse out all of the options from the config file, if they are present
translated_models = filenames.get_models(models_base, 'translated')
untranslated_models = filenames.get_models(models_base, 'untranslated')
translated_models_str = ' '.join(translated_models)
untranslated_models_str = ' '.join(untranslated_models)
translated_models_str = "--translated-models {}".format(
translated_models_str)
untranslated_models_str = "--untranslated-models {}".format(
untranslated_models_str)
orf_types_str = utils.get_config_argument(config, 'orf_types')
seed_str = utils.get_config_argument(config, 'seed')
chains_str = utils.get_config_argument(config, 'chains', 'chains')
iterations_str = utils.get_config_argument(config,
'translation_iterations',
'iterations')
chi_square_only_str = ""
chi_square_only = False
if 'chi_square_only' in config:
chi_square_only = True
chi_square_only_str = "--chi-square-only"
cmd = (
"estimate-orf-bayes-factors {} {} {} {} {} {} {} {} {} {} {} {} {} {} {} {} "
"--num-cpus {}".format(profiles, orfs_genomic, bayes_factors,
translated_models_str, untranslated_models_str,
logging_str, orf_types_str, min_length_str,
max_length_str, min_profile_str, fraction_str,
reweighting_iterations_str, seed_str,
iterations_str, chains_str, chi_square_only_str,
args.num_cpus))
in_files = [profiles, orfs_genomic]
in_files.extend(translated_models)
in_files.extend(untranslated_models)
out_files = [bayes_factors]
file_checkers = {bayes_factors: utils.check_gzip_file}
msg = "estimate-bayes-factors in_files: {}".format(in_files)
logger.debug(msg)
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
is_chisq_values = [True, False]
if chi_square_only:
is_chisq_values = [True]
for is_filtered in [True, False]:
for is_chisq in is_chisq_values:
filtered_str = ""
if is_filtered:
filtered_str = "--select-longest-by-stop --select-best-overlapping"
if is_chisq:
chisq_str = "--use-chi-square"
else:
chisq_str = ""
# now, select the ORFs (longest for each stop codon) which pass the prediction filters
predicted_orfs = filenames.get_riboseq_predicted_orfs(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=is_chisq)
predicted_orfs_dna = filenames.get_riboseq_predicted_orfs_dna(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=is_chisq)
predicted_orfs_protein = filenames.get_riboseq_predicted_orfs_protein(
config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note_str,
fraction=fraction,
reweighting_iterations=reweighting_iterations,
is_filtered=is_filtered,
is_chisq=is_chisq)
min_bf_mean_str = utils.get_config_argument(config, 'min_bf_mean')
max_bf_var_str = utils.get_config_argument(config, 'max_bf_var')
min_bf_likelihood_str = utils.get_config_argument(
config, 'min_bf_likelihood')
chisq_significance_level_str = utils.get_config_argument(
config, 'chisq_significance_level')
min_profile_str = utils.get_config_argument(
config, 'min_signal', 'minimum-profile-sum')
cmd = "select-final-prediction-set {} {} {} {} {} {} {} {} {} {} {}".format(
bayes_factors, config['fasta'], predicted_orfs,
predicted_orfs_dna, predicted_orfs_protein, min_bf_mean_str,
max_bf_var_str, min_bf_likelihood_str, logging_str, chisq_str,
filtered_str)
in_files = [bayes_factors, config['fasta']]
out_files = [
predicted_orfs, predicted_orfs_dna, predicted_orfs_protein
]
file_checkers = {predicted_orfs: utils.check_gzip_file}
# todo: implement file checker for fasta files
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script runs all of the processing necessary to produce the "
"signals used for later processing. In particular, it runs the standard "
"rnaseq and riboseq preprocessing, estimates the abundance of transcripts with "
"the rnaseq data, and selects the most-expressed isoforms and ORFs. Next, it removes "
"multimapping and non-periodic-length riboseq reads. Finally, it extracts the riboseq "
"signal for the most-expressed transcripts.")
parser.add_argument('raw_data', help="The raw data file (fastq[.gz])")
parser.add_argument('config', help="The (json) config file")
parser.add_argument('name', help="The name for the dataset, used in the created files")
parser.add_argument('-p', '--num-cpus', help="The number of processors to use",
type=int, default=default_num_cpus)
parser.add_argument('--mem', help="The amount of RAM to request",
default=default_mem)
parser.add_argument('--flexbar-options', help="A space-delimited list of options to"
"pass to flexbar. Each option must be quoted separately as in \"--flexbarOption value\""
"If specified, flexbar options will override default settings.", nargs='*', type=str)
parser.add_argument('--tmp', help="The location for temp files", default=default_tmp)
parser.add_argument('--do-not-call', action='store_true')
parser.add_argument('--overwrite', help="If this flag is present, existing files "
"will be overwritten.", action='store_true')
parser.add_argument('-k', '--keep-intermediate-files', help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.", action='store_true')
star_utils.add_star_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
msg = "[create-orf-profiles]: {}".format(' '.join(sys.argv))
logger.info(msg)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [ 'flexbar',
args.star_executable,
'samtools',
'bowtie2',
'create-base-genome-profile',
'remove-multimapping-reads',
'extract-metagene-profiles',
'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets',
'extract-orf-profiles'
]
shell_utils.check_programs_exist(programs)
required_keys = [ 'riboseq_data',
'ribosomal_index',
'gtf',
'genome_base_path',
'genome_name'
]
utils.check_keys_exist(config, required_keys)
note = config.get('note', None)
star_index = filenames.get_star_index(config['genome_base_path'],
config['genome_name'], is_merged=False)
models_base = config.get('models_base', default_models_base)
# the first step is the standard riboseq preprocessing
# handle do_not_call so that we _do_ call the preprocessing script,
# but that it does not run anything
do_not_call_argument = ""
if not call:
do_not_call_argument = "--do-not-call"
overwrite_argument = ""
if args.overwrite:
overwrite_argument = "--overwrite"
orfs_genomic = filenames.get_orfs(config['genome_base_path'], config['genome_name'],
note=config.get('orf_note'))
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_option_str = ""
if args.flexbar_options is not None:
flexbar_option_str = "--flexbar-options {}".format(' '.join('"' + flx_op + '"'
for flx_op in args.flexbar_options))
# check if we want to keep multimappers
is_unique = not ('keep_riboseq_multimappers' in config)
riboseq_raw_data = args.raw_data
riboseq_bam_filename = filenames.get_riboseq_bam(config['riboseq_data'], args.name,
is_unique=is_unique, note=note)
mem_str = "--mem {}".format(shlex.quote(args.mem))
cmd = ("create-base-genome-profile {} {} {} --num-cpus {} {} {} {} {} {} {} {} {}"
.format(riboseq_raw_data, args.config, args.name, args.num_cpus,
do_not_call_argument, overwrite_argument, logging_str, star_str, tmp_str,
flexbar_option_str, keep_intermediate_str, mem_str))
# There could be cases where we start somewhere in the middle of creating
# the base genome profile. So even if the "raw data" is not available,
# we still want to call the base pipeline.
#in_files = [riboseq_raw_data]
in_files = []
out_files = [riboseq_bam_filename]
# we always call this, and pass --do-not-call through
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
overwrite=args.overwrite, call=True)
# create the metagene profiles
metagene_profiles = filenames.get_metagene_profiles(config['riboseq_data'],
args.name, is_unique=is_unique, note=note)
start_upstream_str = utils.get_config_argument(config,
'metagene_profile_start_upstream', 'start-upstream')
start_downstream_str = utils.get_config_argument(config,
'metagene_profile_start_downstream', 'start-downstream')
end_upstream_str = utils.get_config_argument(config,
'metagene_profile_end_upstream', 'end-upstream')
end_downstream_str = utils.get_config_argument(config,
'metagene_profile_end_downstream', 'end-downstream')
# use the canonical transcripts for extracting the metagene profiles
transcript_bed = filenames.get_bed(config['genome_base_path'],
config['genome_name'], is_merged=False, is_annotated=True)
cmd = ("extract-metagene-profiles {} {} {} --num-cpus {} {} {} {} {} {}"
.format(riboseq_bam_filename, transcript_bed, metagene_profiles,
args.num_cpus, logging_str, start_upstream_str,
start_downstream_str, end_upstream_str, end_downstream_str))
in_files = [riboseq_bam_filename, orfs_genomic]
out_files = [metagene_profiles]
file_checkers = {
metagene_profiles: utils.check_gzip_file
}
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
file_checkers=file_checkers, overwrite=args.overwrite, call=call)
# estimate the periodicity for each offset for all read lengths
metagene_profile_bayes_factors = filenames.get_metagene_profiles_bayes_factors(
config['riboseq_data'], args.name, is_unique=is_unique, note=note)
#periodic_models_str = utils.get_config_argument(config, 'periodic_models')
#non_periodic_models_str = utils.get_config_argument(config, 'nonperiodic_models')
periodic_models = filenames.get_models(models_base, 'periodic')
non_periodic_models = filenames.get_models(models_base, 'nonperiodic')
periodic_models_str = ' '.join(periodic_models)
non_periodic_models_str = ' '.join(non_periodic_models)
periodic_models_str = "--periodic-models {}".format(periodic_models_str)
non_periodic_models_str = "--nonperiodic-models {}".format(non_periodic_models_str)
periodic_offset_start_str = utils.get_config_argument(config, 'periodic_offset_start')
periodic_offset_end_str = utils.get_config_argument(config, 'periodic_offset_end')
metagene_profile_length_str = utils.get_config_argument(config, 'metagene_profile_length')
seed_str = utils.get_config_argument(config, 'seed')
chains_str = utils.get_config_argument(config, 'chains')
iterations_str = utils.get_config_argument(config, 'metagene_profile_iterations', 'iterations')
cmd = ("estimate-metagene-profile-bayes-factors {} {} --num-cpus {} {} {} "
"{} {} {} {} {} {} {}".format(metagene_profiles,
metagene_profile_bayes_factors, args.num_cpus,
periodic_models_str, non_periodic_models_str,
periodic_offset_start_str, periodic_offset_end_str, metagene_profile_length_str,
seed_str, chains_str, iterations_str, logging_str))
in_files = [metagene_profiles]
in_files.extend(periodic_models)
in_files.extend(non_periodic_models)
out_files = [metagene_profile_bayes_factors]
file_checkers = {
metagene_profile_bayes_factors: utils.check_gzip_file
}
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
file_checkers=file_checkers, overwrite=args.overwrite, call=call)
# select the best read lengths for constructing the signal
periodic_offsets = filenames.get_periodic_offsets(config['riboseq_data'],
args.name, is_unique=is_unique, note=note)
cmd = "select-periodic-offsets {} {}".format(metagene_profile_bayes_factors,
periodic_offsets)
in_files = [metagene_profile_bayes_factors]
out_files = [periodic_offsets]
file_checkers = {
periodic_offsets: utils.check_gzip_file
}
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
file_checkers=file_checkers, overwrite=args.overwrite, call=call)
# get the lengths and offsets which meet the required criteria from the config file
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(config,
args.name, args.do_not_call, is_unique=is_unique)
if len(lengths) == 0:
msg = ("No periodic read lengths and offsets were found. Try relaxing "
"min_metagene_profile_count, min_metagene_bf_mean, max_metagene_bf_var, "
"and/or min_metagene_bf_likelihood. Qutting.")
logger.critical(msg)
return
lengths_str = ' '.join(lengths)
offsets_str = ' '.join(offsets)
seqname_prefix_str = utils.get_config_argument(config, 'seqname_prefix')
# extract the riboseq profiles for each orf
unique_filename = filenames.get_riboseq_bam(config['riboseq_data'], args.name,
is_unique=is_unique, note=note)
profiles_filename = filenames.get_riboseq_profiles(config['riboseq_data'], args.name,
length=lengths, offset=offsets, is_unique=is_unique, note=note)
orfs_genomic = filenames.get_orfs(config['genome_base_path'], config['genome_name'],
note=config.get('orf_note'))
exons_file = filenames.get_exons(config['genome_base_path'], config['genome_name'],
note=config.get('orf_note'), is_orf=True)
cmd = ("extract-orf-profiles {} {} {} {} --lengths {} --offsets {} {} {} --num-cpus {} ".format(
unique_filename, orfs_genomic, exons_file, profiles_filename, lengths_str,
offsets_str, logging_str, seqname_prefix_str, args.num_cpus))
in_files = [orfs_genomic, exons_file, unique_filename]
out_files = [profiles_filename]
#todo: implement a file checker for mtx files
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
overwrite=args.overwrite, call=call)
def main():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description="This script creates all of the files necessary for downstream "
"analysis performed with the rpbp package.")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--overwrite', help="If this flag is present, existing files "
"will be overwritten.", action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'extract-orf-coordinates',
'label-orfs',
'bowtie2-build-s',
'split-bed12-blocks',
'gtf-to-bed12',
args.star_executable
]
shell_utils.check_programs_exist(programs)
required_keys = [ 'genome_base_path',
'genome_name',
'gtf',
'fasta',
'ribosomal_fasta',
'ribosomal_index',
'star_index'
]
utils.check_keys_exist(config, required_keys)
# check that the required files are present
files = [
config['gtf'],
config['fasta'],
config['ribosomal_fasta']
]
if 'de_novo_gtf' in config:
files += [config['de_novo_gtf']]
utils.check_files_exist(files, source='prepare-rpbp-genome')
# now, check if we want to use slurm
if args.use_slurm:
cmd = ' '.join(sys.argv)
slurm.check_sbatch(cmd, args=args)
return
# the rrna index
cmd = "bowtie2-build-s {} {}".format(config['ribosomal_fasta'],
config['ribosomal_index'])
in_files = [config['ribosomal_fasta']]
out_files = bio.get_bowtie2_index_files(config['ribosomal_index'])
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
overwrite=args.overwrite, call=call)
# the STAR index
mem = utils.human2bytes(args.mem)
cmd = ("{} --runMode genomeGenerate --genomeDir {} --genomeFastaFiles {} "
"--runThreadN {} --limitGenomeGenerateRAM {}".format(args.star_executable,
config['star_index'], config['fasta'], args.num_cpus, mem))
in_files = [config['fasta']]
out_files = star_utils.get_star_index_files(config['star_index'])
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
overwrite=args.overwrite, call=call)
# get the main orfs
get_orfs(config['gtf'], args, config, is_annotated=True, is_de_novo=False)
# eventually, we will use these names
annotated_orfs = filenames.get_orfs(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'), is_annotated=True,
is_de_novo=False)
annotated_exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'),
is_annotated=True, is_de_novo=False, is_orf=True)
orfs_genomic = filenames.get_orfs(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'))
exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'), is_orf=True)
use_gff3_specs = config['gtf'].endswith('gff')
gtf_file = filenames.get_gtf(config['genome_base_path'],
config['genome_name'], is_gff3=use_gff3_specs, is_star_input=True)
# now, check if we have a de novo assembly
if 'de_novo_gtf' in config:
get_orfs(config['de_novo_gtf'], args, config, is_annotated=False,
is_de_novo=True)
# we need to concat the ORF and exon files
de_novo_orfs = filenames.get_orfs(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'), is_annotated=False,
is_de_novo=True)
de_novo_exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'], note=config.get('orf_note'),
is_annotated=False, is_de_novo=True, is_orf=True)
orfs_files = [annotated_orfs, de_novo_orfs]
orfs_files_str = ' '.join(orfs_files)
msg = ("Concatenating files. Output file: {}; Input files: {}".format(
orfs_genomic, orfs_files_str))
logger.info(msg)
if call:
concatenated_bed = bed_utils.concatenate(orfs_files, sort_bed=True)
concatenated_bed['orf_num'] = range(len(concatenated_bed))
fields = bed_utils.bed12_field_names + ['orf_num', 'orf_len', 'orf_type']
bed_utils.write_bed(concatenated_bed[fields], orfs_genomic)
else:
msg = "Skipping concatenation due to --call value"
logger.info(msg)
exons_files = [annotated_exons_file, de_novo_exons_file]
exons_files_str = ' '.join(exons_files)
msg = ("Concatenating files. Output file: {}; Input files: {}".format(
exons_file, exons_files_str))
logger.info(msg)
if call:
concatenated_bed = bed_utils.concatenate(exons_files, sort_bed=True)
fields = bed_utils.bed6_field_names + ['exon_index', 'transcript_start']
bed_utils.write_bed(concatenated_bed[fields], exons_file)
else:
msg = "Skipping concatenation due to --call value"
logger.info(msg)
# we also need to concat the annotations to inform STAR
# there is no particular reason to merge and sort the files, so
# we just concatenate them...
if (config['de_novo_gtf'].endswith('gff') == use_gff3_specs):
cmd = ("awk '!/^#/' {} {} > {}".format(config['gtf'], config['de_novo_gtf'], gtf_file))
in_files = [config['gtf'], config['de_novo_gtf']]
out_files = [gtf_file]
shell_utils.call_if_not_exists(cmd, out_files, in_files=in_files,
overwrite=args.overwrite, call=call)
else:
msg = ("Skipping concatenation due to mismatch in format specifications (GTF2/GFF3)"
"for reference and do novo annotations. Symlink to reference annotations created.")
logger.warning(msg)
if os.path.exists(config['gtf']):
shell_utils.create_symlink(config['gtf'], gtf_file, call)
else:
# finally, make sure our files are named correctly
if os.path.exists(annotated_orfs):
shell_utils.create_symlink(annotated_orfs, orfs_genomic, call)
if os.path.exists(annotated_exons_file):
shell_utils.create_symlink(annotated_exons_file, exons_file, call)
if os.path.exists(config['gtf']):
shell_utils.create_symlink(config['gtf'], gtf_file, call)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This script runs all of the processing necessary to produce the "
"signals used for later processing. In particular, it runs the standard "
"rnaseq and riboseq preprocessing, estimates the abundance of transcripts with "
"the rnaseq data, and selects the most-expressed isoforms and ORFs. Next, it removes "
"multimapping and non-periodic-length riboseq reads. Finally, it extracts the riboseq "
"signal for the most-expressed transcripts.")
parser.add_argument('raw_data', help="The raw data file (fastq[.gz])")
parser.add_argument('config', help="The (json) config file")
parser.add_argument(
'name', help="The name for the dataset, used in the created files")
parser.add_argument('-p',
'--num-cpus',
help="The number of processors to use",
type=int,
default=default_num_cpus)
parser.add_argument('--mem',
help="The amount of RAM to request",
default=default_mem)
parser.add_argument(
'--flexbar-format-option',
help="The name of the \"format\" "
"option for flexbar. This changed from \"format\" to \"qtrim-format\" in "
"version 2.7.",
default=default_flexbar_format_option)
parser.add_argument('--tmp',
help="The location for temp files",
default=default_tmp)
parser.add_argument('--do-not-call', action='store_true')
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
parser.add_argument(
'-k',
'--keep-intermediate-files',
help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.",
action='store_true')
star_utils.add_star_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
msg = "[create-orf-profiles]: {}".format(' '.join(sys.argv))
logger.info(msg)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar', args.star_executable, 'samtools', 'bowtie2',
'create-base-genome-profile', 'remove-multimapping-reads',
'extract-metagene-profiles', 'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets', 'extract-orf-profiles'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data', 'ribosomal_index', 'gtf', 'genome_base_path',
'genome_name'
]
utils.check_keys_exist(config, required_keys)
note = config.get('note', None)
star_index = filenames.get_star_index(config['genome_base_path'],
config['genome_name'],
is_merged=False)
models_base = config.get('models_base', default_models_base)
# the first step is the standard riboseq preprocessing
# handle do_not_call so that we _do_ call the preprocessing script,
# but that it does not run anything
do_not_call_argument = ""
if not call:
do_not_call_argument = "--do-not-call"
overwrite_argument = ""
if args.overwrite:
overwrite_argument = "--overwrite"
orfs_genomic = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_format_option_str = ""
if args.flexbar_format_option is not None:
flexbar_format_option_str = "--flexbar-format-option {}".format(
args.flexbar_format_option)
# check if we want to keep multimappers
is_unique = not ('keep_riboseq_multimappers' in config)
riboseq_raw_data = args.raw_data
riboseq_bam_filename = filenames.get_riboseq_bam(config['riboseq_data'],
args.name,
is_unique=is_unique,
note=note)
mem_str = "--mem {}".format(shlex.quote(args.mem))
cmd = (
"create-base-genome-profile {} {} {} --num-cpus {} {} {} {} {} {} {} {} {}"
.format(riboseq_raw_data, args.config, args.name, args.num_cpus,
do_not_call_argument, overwrite_argument, logging_str,
star_str, tmp_str, flexbar_format_option_str,
keep_intermediate_str, mem_str))
# There could be cases where we start somewhere in the middle of creating
# the base genome profile. So even if the "raw data" is not available,
# we still want to call the base pipeline.
#in_files = [riboseq_raw_data]
in_files = []
out_files = [riboseq_bam_filename]
# we always call this, and pass --do-not-call through
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=True)
# create the metagene profiles
metagene_profiles = filenames.get_metagene_profiles(config['riboseq_data'],
args.name,
is_unique=is_unique,
note=note)
seqids_to_keep_str = utils.get_config_argument(config, 'seqids_to_keep')
start_upstream_str = utils.get_config_argument(
config, 'metagene_profile_start_upstream', 'start-upstream')
start_downstream_str = utils.get_config_argument(
config, 'metagene_profile_start_downstream', 'start-downstream')
end_upstream_str = utils.get_config_argument(
config, 'metagene_profile_end_upstream', 'end-upstream')
end_downstream_str = utils.get_config_argument(
config, 'metagene_profile_end_downstream', 'end-downstream')
# use the canonical transcripts for extracting the metagene profiles
transcript_bed = filenames.get_bed(config['genome_base_path'],
config['genome_name'],
is_merged=False,
is_annotated=True)
cmd = ("extract-metagene-profiles {} {} {} --num-cpus {} {} {} {} {} {} {}"
.format(riboseq_bam_filename, transcript_bed, metagene_profiles,
args.num_cpus, logging_str, seqids_to_keep_str,
start_upstream_str, start_downstream_str, end_upstream_str,
end_downstream_str))
in_files = [riboseq_bam_filename, orfs_genomic]
out_files = [metagene_profiles]
file_checkers = {metagene_profiles: utils.check_gzip_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
# estimate the periodicity for each offset for all read lengths
metagene_profile_bayes_factors = filenames.get_metagene_profiles_bayes_factors(
config['riboseq_data'], args.name, is_unique=is_unique, note=note)
#periodic_models_str = utils.get_config_argument(config, 'periodic_models')
#non_periodic_models_str = utils.get_config_argument(config, 'nonperiodic_models')
periodic_models = filenames.get_models(models_base, 'periodic')
non_periodic_models = filenames.get_models(models_base, 'nonperiodic')
periodic_models_str = ' '.join(periodic_models)
non_periodic_models_str = ' '.join(non_periodic_models)
periodic_models_str = "--periodic-models {}".format(periodic_models_str)
non_periodic_models_str = "--nonperiodic-models {}".format(
non_periodic_models_str)
periodic_offset_start_str = utils.get_config_argument(
config, 'periodic_offset_start')
periodic_offset_end_str = utils.get_config_argument(
config, 'periodic_offset_end')
metagene_profile_length_str = utils.get_config_argument(
config, 'metagene_profile_length')
seed_str = utils.get_config_argument(config, 'seed')
chains_str = utils.get_config_argument(config, 'chains')
iterations_str = utils.get_config_argument(config,
'metagene_profile_iterations',
'iterations')
cmd = ("estimate-metagene-profile-bayes-factors {} {} --num-cpus {} {} {} "
"{} {} {} {} {} {} {}".format(
metagene_profiles, metagene_profile_bayes_factors,
args.num_cpus, periodic_models_str, non_periodic_models_str,
periodic_offset_start_str, periodic_offset_end_str,
metagene_profile_length_str, seed_str, chains_str,
iterations_str, logging_str))
in_files = [metagene_profiles]
in_files.extend(periodic_models)
in_files.extend(non_periodic_models)
out_files = [metagene_profile_bayes_factors]
file_checkers = {metagene_profile_bayes_factors: utils.check_gzip_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
# select the best read lengths for constructing the signal
periodic_offsets = filenames.get_periodic_offsets(config['riboseq_data'],
args.name,
is_unique=is_unique,
note=note)
cmd = "select-periodic-offsets {} {}".format(
metagene_profile_bayes_factors, periodic_offsets)
in_files = [metagene_profile_bayes_factors]
out_files = [periodic_offsets]
file_checkers = {periodic_offsets: utils.check_gzip_file}
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
file_checkers=file_checkers,
overwrite=args.overwrite,
call=call)
# get the lengths and offsets which meet the required criteria from the config file
lengths, offsets = ribo_utils.get_periodic_lengths_and_offsets(
config, args.name, args.do_not_call, is_unique=is_unique)
if len(lengths) == 0:
msg = (
"No periodic read lengths and offsets were found. Try relaxing "
"min_metagene_profile_count, min_metagene_bf_mean, max_metagene_bf_var, "
"and/or min_metagene_bf_likelihood. Qutting.")
logger.critical(msg)
return
lengths_str = ' '.join(lengths)
offsets_str = ' '.join(offsets)
seqname_prefix_str = utils.get_config_argument(config, 'seqname_prefix')
# extract the riboseq profiles for each orf
unique_filename = filenames.get_riboseq_bam(config['riboseq_data'],
args.name,
is_unique=is_unique,
note=note)
profiles_filename = filenames.get_riboseq_profiles(config['riboseq_data'],
args.name,
length=lengths,
offset=offsets,
is_unique=is_unique,
note=note)
orfs_genomic = filenames.get_orfs(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
exons_file = filenames.get_exons(config['genome_base_path'],
config['genome_name'],
note=config.get('orf_note'))
cmd = (
"extract-orf-profiles {} {} {} {} --lengths {} --offsets {} {} {} --num-cpus {} "
.format(unique_filename, orfs_genomic, exons_file, profiles_filename,
lengths_str, offsets_str, logging_str, seqname_prefix_str,
args.num_cpus))
in_files = [orfs_genomic, exons_file, unique_filename]
out_files = [profiles_filename]
#todo: implement a file checker for mtx files
shell_utils.call_if_not_exists(cmd,
out_files,
in_files=in_files,
overwrite=args.overwrite,
call=call)
def main():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description=
"This is a helper script which submits a set of samples to SLURM. It "
"can also be used to run a set of samples sequentially. Due to limitations on "
"the config file specification, all of the samples must use the same reference "
"indices (i.e., genome sequence, set of ORFs, etc.).")
parser.add_argument('config', help="The (yaml) config file")
parser.add_argument('--tmp',
help="The temp directory",
default=default_tmp)
parser.add_argument(
'--flexbar-format-option',
help="The name of the \"format\" "
"option for flexbar. This changed from \"format\" to \"qtrim-format\" in "
"version 2.7.",
default=default_flexbar_format_option)
parser.add_argument('--overwrite',
help="If this flag is present, existing files "
"will be overwritten.",
action='store_true')
parser.add_argument(
'--merge-replicates',
help="If this flag is present, then "
"the ORF profiles from the replicates will be merged before making the final "
"predictions",
action='store_true')
parser.add_argument(
'--run-replicates',
help="If this flag is given with the "
"--merge-replicates flag, then both the replicates *and* the individual "
"samples will be run. This flag has no effect if --merge-replicates is not "
"given.",
action='store_true')
parser.add_argument(
'-k',
'--keep-intermediate-files',
help="If this flag is given, "
"then all intermediate files will be kept; otherwise, they will be "
"deleted. This feature is implemented piecemeal. If the --do-not-call flag "
"is given, then nothing will be deleted.",
action='store_true')
star_utils.add_star_options(parser)
slurm.add_sbatch_options(parser)
logging_utils.add_logging_options(parser)
args = parser.parse_args()
logging_utils.update_logging(args)
logging_str = logging_utils.get_logging_options_string(args)
star_str = star_utils.get_star_options_string(args)
config = yaml.load(open(args.config))
call = not args.do_not_call
# check that all of the necessary programs are callable
programs = [
'flexbar', args.star_executable, 'samtools', 'bowtie2',
'create-base-genome-profile', 'remove-multimapping-reads',
'extract-metagene-profiles', 'estimate-metagene-profile-bayes-factors',
'select-periodic-offsets', 'extract-orf-profiles',
'estimate-orf-bayes-factors', 'select-final-prediction-set',
'create-orf-profiles', 'predict-translated-orfs', 'run-rpbp-pipeline'
]
shell_utils.check_programs_exist(programs)
required_keys = [
'riboseq_data', 'riboseq_samples', 'ribosomal_index', 'star_index',
'genome_base_path', 'genome_name', 'fasta', 'gtf'
]
utils.check_keys_exist(config, required_keys)
note = config.get('note', None)
# handle do_not_call so that we _do_ call the pipeline script, but that it does not run anything
do_not_call_str = ""
if not call:
do_not_call_str = "--do-not-call"
args.do_not_call = False
overwrite_str = ""
if args.overwrite:
overwrite_str = "--overwrite"
mem_str = "--mem {}".format(shlex.quote(args.mem))
keep_intermediate_str = ""
if args.keep_intermediate_files:
keep_intermediate_str = "--keep-intermediate-files"
# if we merge the replicates, then we only use the rpbp script to create
# the ORF profiles
profiles_only_str = ""
if args.merge_replicates and not args.run_replicates:
profiles_only_str = "--profiles-only"
if args.run_replicates and not args.merge_replicates:
msg = (
"The --run-replicates option was given with the --merge-replicates "
"option. It will be ignored.")
logger.warning(msg)
tmp_str = ""
if args.tmp is not None:
tmp_str = "--tmp {}".format(args.tmp)
flexbar_format_option_str = ""
if args.flexbar_format_option is not None:
flexbar_format_option_str = "--flexbar-format-option {}".format(
args.flexbar_format_option)
# collect the job_ids in case we are using slurm and need to merge replicates
job_ids = []
sample_names = sorted(config['riboseq_samples'].keys())
for sample_name in sample_names:
data = config['riboseq_samples'][sample_name]
tmp_str = ""
if args.tmp is not None:
tmp = os.path.join(args.tmp,
"{}_{}_rpbp".format(sample_name, note))
tmp_str = "--tmp {}".format(tmp)
cmd = "run-rpbp-pipeline {} {} {} --num-cpus {} {} {} {} {} {} {} {} {} {}".format(
data, args.config, sample_name, args.num_cpus, tmp_str,
do_not_call_str, overwrite_str, logging_str, star_str,
profiles_only_str, flexbar_format_option_str,
keep_intermediate_str, mem_str)
job_id = slurm.check_sbatch(cmd, args=args)
job_ids.append(job_id)
# now, if we are running the "standard" pipeline, we are finished
if not args.merge_replicates:
return
# otherwise, we need to merge the replicates for each condition
riboseq_replicates = ribo_utils.get_riboseq_replicates(config)
merge_replicates_str = "--merge-replicates"
for condition_name in sorted(riboseq_replicates.keys()):
# then we predict the ORFs
cmd = "predict-translated-orfs {} {} --num-cpus {} {} {} {} {}".format(
args.config, condition_name, args.num_cpus, do_not_call_str,
overwrite_str, logging_str, merge_replicates_str)
slurm.check_sbatch(cmd, args=args, dependencies=job_ids)