def proc_args(argv):
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input. ' \
'Usage: ' + basename(__file__) + ' sample2bam.tsv --bed target.bed --contols sample1:sample2 -o results_dir'
parser = OptionParser(description=description, usage=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('-o', dest='output_dir', metavar='DIR', default=join(os.getcwd(), 'seq2c'))
parser.add_option('--bed', dest='bed', help='BED file to run Seq2C analysis')
parser.add_option('-c', '--controls', dest='controls', help='Optional control sample names for Seq2C. For multiple controls, separate them using :')
parser.add_option('--seq2c-opts', dest='seq2c_opts', help='Options for the final lr2gene.pl script.')
parser.add_option('--no-prep-bed', dest='prep_bed', help=SUPPRESS_HELP, action='store_false', default=True)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
parser.print_usage()
sys.exit(1)
if len(args) == 1 and not args[0].endswith('.bam'):
sample_names, bam_fpaths = read_samples(verify_file(args[0], is_critical=True, description='Input sample2bam.tsv'))
bam_by_sample = OrderedDict()
for s, b in zip(sample_names, bam_fpaths):
bam_by_sample[s] = b
else:
bam_by_sample = find_bams(args)
run_cnf = determine_run_cnf(opts, is_wgs=not opts.__dict__.get('bed'))
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
check_genome_resources(cnf)
cnf.output_dir = adjust_path(cnf.output_dir)
verify_dir(dirname(cnf.output_dir), is_critical=True)
safe_mkdir(cnf.output_dir)
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'Seq2C'
set_up_dirs(cnf)
samples = [
source.TargQC_Sample(name=s_name, dirpath=join(cnf.output_dir, s_name), bam=bam_fpath)
for s_name, bam_fpath in bam_by_sample.items()]
info('Samples: ')
for s in samples:
info(' ' + s.name)
samples.sort(key=lambda _s: _s.key_to_sort())
target_bed = verify_bed(cnf.bed, is_critical=True) if cnf.bed else None
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner: critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
return cnf, samples, target_bed, cnf.output_dir
def proc_opts():
parser = OptionParser()
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('--expose-only',
dest='expose_to_ngs_server_only',
action='store_true',
default=False,
help='Only add project to the webserver')
parser.add_option('--no-expose',
dest='expose',
action='store_false',
default=True,
help='Do not expose the reports')
parser.add_option('-o', dest='output_dir')
parser.add_option('--bed',
dest='bed',
help='BED file to run targetSeq and Seq2C analysis on.')
parser.add_option('--downsample-to', dest='downsample_to', type='int')
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) < 1:
critical('Usage: ' + __file__ + ' *.fq.gz -o output_dir')
# if len(args) < 2:
# info('No dataset path specified, assuming it is the current working directory')
# dataset_dirpath = adjust_path(os.getcwd())
# jira_url = args[0]
fastq_fpaths = [verify_file(fpath) for fpath in args]
fastq_fpaths = [fpath for fpath in fastq_fpaths if fpath]
info(str(len(fastq_fpaths)) + ' fastq files')
run_cnf = determine_run_cnf(opts)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
cnf.output_dir = adjust_path(cnf.output_dir)
info('Writing to ' + str(cnf.output_dir))
cnf.project_name = cnf.project_name or 'preproc'
if cnf.work_dir:
cnf.debug = True
else:
all_work_dir = join(cnf.output_dir, 'work')
safe_mkdir(all_work_dir)
latest_fpath = join(all_work_dir, 'latest')
if cnf.reuse_intermediate:
cnf.work_dir = latest_fpath
else:
cnf.work_dir = join(
all_work_dir,
datetime.datetime.now().strftime("%Y-%b-%d_%H-%M"))
if islink(latest_fpath):
os.remove(latest_fpath)
if isdir(latest_fpath):
shutil.rmtree(latest_fpath)
if not exists(latest_fpath):
os.symlink(basename(cnf.work_dir), latest_fpath)
cnf.work_dir = adjust_path(cnf.work_dir)
safe_mkdir(cnf.work_dir)
cnf.log_dir = join(cnf.work_dir, 'log')
safe_mkdir(cnf.log_dir)
set_up_log(cnf)
try:
subprocess.call(['chmod', '-R', 'g+w', cnf.work_dir])
except OSError:
err(traceback.format_exc())
pass
if cnf.samplesheet:
cnf.samplesheet = verify_file(cnf.samplesheet, is_critical=True)
info(' '.join(sys.argv))
info()
info('Created a temporary working directory: ' + cnf.work_dir)
if cnf.project_name:
info('Project name: ' + cnf.project_name)
if cnf.samplesheet:
info('Using custom sample sheet ' + cnf.samplesheet)
check_genome_resources(cnf)
check_system_resources(cnf, optional=['fastq'])
return cnf, cnf.output_dir, fastq_fpaths
def main():
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input.'
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser, threads=1)
parser.add_option('--work-dir', dest='work_dir', metavar='DIR')
parser.add_option('--log-dir', dest='log_dir')
parser.add_option('--only-summary',
dest='only_summary',
action='store_true')
parser.add_option('-o',
dest='output_dir',
metavar='DIR',
default=join(os.getcwd(), 'targetqc'))
parser.add_option('--reannotate',
dest='reannotate',
action='store_true',
default=False,
help='re-annotate BED file with gene names')
parser.add_option('--dedup',
dest='dedup',
action='store_true',
default=False,
help='count duplicates in coverage metrics')
parser.add_option('--bed',
dest='bed',
help='BED file to run targetSeq and Seq2C analysis on.')
parser.add_option(
'--exons',
'--exome',
'--features',
dest='features',
help=
'Annotated CDS/Exon/Gene/Transcripts BED file to make targetSeq exon/amplicon regions reports.'
)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
critical('No BAMs provided to input.')
bam_fpaths = list(set([abspath(a) for a in args]))
bad_bam_fpaths = []
for fpath in bam_fpaths:
if not verify_bam(fpath):
bad_bam_fpaths.append(fpath)
if bad_bam_fpaths:
critical('BAM files cannot be found, empty or not BAMs:' +
', '.join(bad_bam_fpaths))
run_cnf = determine_run_cnf(opts, is_wgs=not opts.__dict__.get('bed'))
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'TargQC'
set_up_dirs(cnf)
# cnf.name = 'TargQC_' + cnf.project_name
check_genome_resources(cnf)
verify_bed(cnf.bed, is_critical=True)
bed_fpath = adjust_path(cnf.bed)
info('Using amplicons/capture panel ' + bed_fpath)
features_bed_fpath = adjust_path(
cnf.features) if cnf.features else adjust_path(cnf.genome.features)
info('Features: ' + features_bed_fpath)
genes_fpath = None
if cnf.genes:
genes_fpath = adjust_path(cnf.genes)
info('Custom genes list: ' + genes_fpath)
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner:
critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
info('*' * 70)
info()
targqc_html_fpath = run_targqc(cnf, cnf.output_dir, bam_fpaths, bed_fpath,
features_bed_fpath, genes_fpath)
if targqc_html_fpath:
send_email(
cnf, 'TargQC report for ' + cnf.project_name + ':\n ' +
targqc_html_fpath)
def proc_args(argv):
info(' '.join(sys.argv))
info()
description = 'This script generates target QC reports for each BAM provided as an input.'
parser = OptionParser(description=description)
add_cnf_t_reuse_prjname_donemarker_workdir_genome_debug(parser)
parser.add_option('--log-dir', dest='log_dir')
parser.add_option('--is-wgs',
dest='is_wgs',
action='store_true',
default=False,
help='whole genome sequencing')
parser.add_option('--is-deep-seq',
dest='is_deep_seq',
action='store_true',
default=False,
help='deep targeted sequencing')
parser.add_option('--only-summary',
dest='only_summary',
action='store_true')
parser.add_option('-o',
dest='output_dir',
metavar='DIR',
default=join(os.getcwd(), 'targetqc'))
parser.add_option('-c', '--caller', dest='caller')
parser.add_option('--qc', dest='qc', action='store_true', default=False)
parser.add_option('--no-qc',
dest='qc',
action='store_false',
default=False)
parser.add_option('--qc-caption', dest='qc_caption', help=SUPPRESS_HELP)
parser.add_option('--no-tsv',
dest='tsv',
action='store_false',
default=True,
help=SUPPRESS_HELP)
(opts, args) = parser.parse_args()
logger.is_debug = opts.debug
if len(args) == 0:
critical('No vcf files provided to input.')
run_cnf = determine_run_cnf(opts,
is_targetseq=opts.is_deep_seq,
is_wgs=opts.is_wgs)
cnf = Config(opts.__dict__, determine_sys_cnf(opts), run_cnf)
vcf_fpath_by_sample = read_samples(args, cnf.caller)
info()
if not cnf.project_name:
cnf.project_name = basename(cnf.output_dir)
info('Project name: ' + cnf.project_name)
cnf.proc_name = 'Variants'
set_up_dirs(cnf)
# cnf.name = 'TargQC_' + cnf.project_name
info(' '.join(sys.argv))
samples = [
source.VarSample(s_name, join(cnf.output_dir, s_name), vcf=vcf_fpath)
for s_name, vcf_fpath in vcf_fpath_by_sample.items()
]
samples.sort(key=lambda _s: _s.key_to_sort())
check_genome_resources(cnf)
if not cnf.only_summary:
cnf.qsub_runner = adjust_system_path(cnf.qsub_runner)
if not cnf.qsub_runner:
critical('Error: qsub-runner is not provided is sys-config.')
verify_file(cnf.qsub_runner, is_critical=True)
return cnf, samples