def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: sys.argv[1:] (actually command-line arguments)
"""
ap = AnnotationParser()
bp = BaseParser()
annotation_parser = ap.get_parser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
parents=[base_parser,annotation_parser],
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("--no_escape",default=True,action="store_false",
help="If specified and output format is GTF2, special characters in column 9 will be escaped (default: True)")
parser.add_argument("--output_format",choices=["BED","GTF2"],default="GTF2",
help="Format of output file. (default: GTF2)")
parser.add_argument("--extra_columns",nargs="+",default=[],type=str,
help="Attributes (e.g. 'gene_id' to output as extra columns in extended BED format (BED output only).")
parser.add_argument("--empty_value",default="na",type=str,
help="Value to use of an attribute in `extra_columns` is not defined for a particular record (Default: 'na'")
parser.add_argument("outfile",metavar="outfile.[ bed | gtf ]",type=str,
help="Output file")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
end_message = ""
extra_cols = args.extra_columns
if extra_cols is not None:
if args.output_format == "BED":
# avoid name clashes
names_used = copy.copy(BED12_RESERVED_NAMES)
asql_names = [fix_name(X,names_used) for X in extra_cols]
autosql_str = "\n".join(AUTOSQL_ROW_FMT_STR % (X," "*max(15-len(X),2)) for X in asql_names)
file_info = {
"outbase" : args.outfile.replace(".bed","").replace(".gtf",""),
"numcols" : len(extra_cols),
"autosql" : DEFAULT_AUTOSQL_STR % (os.path.basename(args.outfile[:-4]),autosql_str),
}
end_message = MAKE_BIGBED_MESSAGE % file_info
else:
warn("`--extra_columns` is ignored for %s-formatted output." % (args.output_format),ArgumentWarning)
with argsopener(args.outfile,args,"w") as fout:
c = 0
transcripts = ap.get_transcripts_from_args(args,printer=printer)
for transcript in transcripts:
if args.output_format == "GTF2":
fout.write(transcript.as_gtf(escape=args.no_escape))
elif args.output_format == "BED":
fout.write(transcript.as_bed(extra_columns=extra_cols,empty_value=args.empty_value))
if c % 1000 == 1:
printer.write("Processed %s transcripts ..." % c)
c += 1
printer.write("Processed %s transcripts total." % c)
printer.write("Done.")
print(end_message)
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
ap = AnnotationParser()
annotation_file_parser = ap.get_parser(conflict_handler="resolve")
al = AlignmentParser(disabled=_DISABLED)
alignment_file_parser = al.get_parser(conflict_handler="resolve")
mp = MaskParser()
mask_file_parser = mp.get_parser()
bp = BaseParser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[base_parser,
alignment_file_parser,
annotation_file_parser,
mask_file_parser],
)
parser.add_argument("outfile",type=str,help="Output filename")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
ga = al.get_genome_array_from_args(args,printer=printer)
transcripts = ap.get_transcripts_from_args(args,printer=printer,return_type=SegmentChain)
crossmap = mp.get_genome_hash_from_args(args,printer=printer)
ga_sum = ga.sum()
normconst = 1000.0*1e6 / ga_sum
with argsopener(args.outfile,args,"w") as fout:
fout.write("## total_dataset_counts: %s\n" % ga_sum)
fout.write("region_name\tregion\tcounts\tcounts_per_nucleotide\trpkm\tlength\n")
for n,ivc in enumerate(transcripts):
name = ivc.get_name()
masks = crossmap.get_overlapping_features(ivc)
ivc.add_masks(*itertools.chain.from_iterable((X for X in masks)))
if n % 1000 == 0:
printer.write("Processed %s regions..." % n)
counts = numpy.nansum(ivc.get_masked_counts(ga))
length = ivc.masked_length
rpnt = numpy.nan if length == 0 else float(counts)/length
rpkm = numpy.nan if length == 0 else rpnt * normconst
ltmp = [name,
str(ivc),
"%.8e" % counts,
"%.8e" % rpnt,
"%.8e" % rpkm,
"%d" % length]
fout.write("%s\n" % "\t".join(ltmp))
fout.close()
printer.write("Processed %s regions total." % n)
printer.write("Done.")
def main(args=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
al = AlignmentParser()
an = AnnotationParser()
mp = MaskParser()
bp = BaseParser()
alignment_file_parser = al.get_parser(conflict_handler="resolve")
annotation_file_parser = an.get_parser(conflict_handler="resolve")
mask_file_parser = mp.get_parser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
conflict_handler="resolve",
parents=[
base_parser, alignment_file_parser, annotation_file_parser,
mask_file_parser
])
parser.add_argument("out_folder",
type=str,
help="Folder in which to save output vectors")
parser.add_argument(
"--out_prefix",
default="",
type=str,
help="Prefix to prepend to output files (default: no prefix)")
parser.add_argument(
"--format",
default="%.8f",
type=str,
help=r"printf-style format string for output (default: '%%.8f')")
args = parser.parse_args(args)
bp.get_base_ops_from_args(args)
# if output folder doesn't exist, create it
if not os.path.isdir(args.out_folder):
os.mkdir(args.out_folder)
# parse args
ga = al.get_genome_array_from_args(args, printer=printer)
transcripts = an.get_segmentchains_from_args(args, printer=printer)
mask_hash = mp.get_genome_hash_from_args(args, printer=printer)
# evaluate
for n, tx in enumerate(transcripts):
if n % 1000 == 0:
printer.write("Processed %s regions of interest" % n)
filename = "%s%s.txt" % (args.out_prefix, tx.get_name())
full_filename = os.path.join(args.out_folder, filename)
# mask out overlapping masked regions
overlapping = mask_hash.get_overlapping_features(tx)
for feature in overlapping:
tx.add_masks(*feature.segments)
count_vec = tx.get_masked_counts(ga)
numpy.savetxt(full_filename, count_vec, fmt=args.format)
def main(args=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
al = AlignmentParser()
an = AnnotationParser()
mp = MaskParser()
bp = BaseParser()
alignment_file_parser = al.get_parser(conflict_handler="resolve")
annotation_file_parser = an.get_parser(conflict_handler="resolve")
mask_file_parser = mp.get_parser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
conflict_handler="resolve",
parents=[base_parser, alignment_file_parser, annotation_file_parser, mask_file_parser],
)
parser.add_argument("out_folder", type=str, help="Folder in which to save output vectors")
parser.add_argument(
"--out_prefix", default="", type=str, help="Prefix to prepend to output files (default: no prefix)"
)
parser.add_argument(
"--format", default="%.8f", type=str, help=r"printf-style format string for output (default: '%%.8f')"
)
args = parser.parse_args(args)
bp.get_base_ops_from_args(args)
# if output folder doesn't exist, create it
if not os.path.isdir(args.out_folder):
os.mkdir(args.out_folder)
# parse args
ga = al.get_genome_array_from_args(args, printer=printer)
transcripts = an.get_segmentchains_from_args(args, printer=printer)
mask_hash = mp.get_genome_hash_from_args(args, printer=printer)
# evaluate
for n, tx in enumerate(transcripts):
if n % 1000 == 0:
printer.write("Processed %s regions of interest" % n)
filename = "%s%s.txt" % (args.out_prefix, tx.get_name())
full_filename = os.path.join(args.out_folder, filename)
# mask out overlapping masked regions
overlapping = mask_hash.get_overlapping_features(tx)
for feature in overlapping:
tx.add_masks(*feature.segments)
count_vec = tx.get_masked_counts(ga)
numpy.savetxt(full_filename, count_vec, fmt=args.format)
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: sys.argv[1:] (actually command-line arguments)
"""
ap = AnnotationParser(input_choices=_ANNOTATION_INPUT_CHOICES)
annotation_file_parser = ap.get_parser()
bp = BaseParser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[base_parser,annotation_file_parser])
parser.add_argument("--export_tophat",default=False,action="store_true",
help="Export tophat `.juncs` file in addition to BED output")
parser.add_argument("outbase",type=str,help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
transcripts = ap.get_transcripts_from_args(args,printer=printer,return_type=SegmentChain)
with argsopener("%s.bed" % args.outbase,args,"w") as bed_out:
if args.export_tophat == True:
tophat_out = open("%s.juncs" % args.outbase,"w")
printer.write("params: " +" ".join(argv))
printer.write("Detecting & comparing junctions...")
ex_pairs = {}
c = 0
u = 0
for chain in transcripts:
if len(chain) > 1: # if multi-exon
chrom = chain.chrom
strand = chain.strand
try:
ep = ex_pairs[(chrom,strand)]
except KeyError:
ex_pairs[(chrom,strand)] = []
ep = ex_pairs[(chrom,strand)]
for i in range(0,len(chain)-1):
seg1 = chain[i]
seg2 = chain[i+1]
if c % 1000 == 0 and c > 0:
printer.write("Processed %s junctions. Found %s unique..." % (c,u) )
c+=1
key = (seg1.end,seg2.start)
if key not in ep:
ep.append(key)
u += 1
new_chain = SegmentChain(seg1,seg2)
bed_out.write(new_chain.as_bed())
if args.export_tophat == True:
my_junc = (chrom,seg1.end-1,seg2.start,strand)
tophat_out.write("%s\t%s\t%s\t%s\n" % my_junc)
del new_chain
del seg1
del seg2
del chain
printer.write("Processed %s total junctions. Found %s unique." % (c,u) )
bed_out.close()
if args.export_tophat == True:
tophat_out.close()
printer.write("Done.")
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
al = AlignmentParser(disabled=["normalize","big_genome","spliced_bowtie_files"],
input_choices=["BAM"])
an = AnnotationParser()
pp = PlottingParser()
bp = BaseParser()
plotting_parser = pp.get_parser()
alignment_file_parser = al.get_parser(conflict_handler="resolve")
annotation_file_parser = an.get_parser(conflict_handler="resolve")
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
conflict_handler="resolve",
parents=[base_parser,
annotation_file_parser,
alignment_file_parser,
plotting_parser])
parser.add_argument("roi_file",type=str,nargs="?",default=None,
help="Optional. ROI file of maximal spanning windows surrounding start codons, "+\
"from ``metagene generate`` subprogram. Using this instead of `--annotation_files` "+\
"prevents double-counting of codons when multiple transcript isoforms exist "+\
"for a gene. See the documentation for `metagene` for more info about ROI files."+\
"If an ROI file is not given, supply an annotation with ``--annotation_files``")
parser.add_argument("outbase",type=str,help="Required. Basename for output files")
parser.add_argument("--codon_buffer",type=int,default=5,
help="Codons before and after start codon to ignore (Default: 5)")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
pp.set_style_from_args(args)
gnd = al.get_genome_array_from_args(args,printer=printer)
read_lengths = list(range(args.min_length,args.max_length+1))
codon_buffer = args.codon_buffer
dtmp = { "read_length" : numpy.array(read_lengths),
"reads_counted" : numpy.zeros_like(read_lengths,dtype=int),
}
if args.roi_file is not None:
using_roi = True
roi_table = read_pl_table(args.roi_file)
regions = roi_table.iterrows()
transform_fn = roi_row_to_cds
back_buffer = -1
if len(args.annotation_files) > 0:
warnings.warn("If an ROI file is given, annotation files are ignored. Pulling regions from '%s'. Ignoring '%s'" % (args.roi_file,
", ".join(args.annotation_files)),
ArgumentWarning)
else:
using_roi = False
if len(args.annotation_files) == 0:
printer.write("Either an ROI file or at least annotation file must be given.")
sys.exit(1)
else:
warnings.warn("Using a transcript annotation file instead of an ROI file can lead to double-counting of codons if the annotation contains multiple transcripts per gene.",
ArgumentWarning)
regions = an.get_transcripts_from_args(args,printer=printer)
back_buffer = -codon_buffer
transform_fn = lambda x: x.get_cds()
phase_sums = {}
for k in read_lengths:
phase_sums[k] = numpy.zeros(3)
for n, roi in enumerate(regions):
if n % 1000 == 1:
printer.write("Counted %s ROIs ..." % n)
# transformation needed to extract CDS from transcript or from ROI file window
cds_part = transform_fn(roi)
# only calculate for coding genes
if len(cds_part) > 0:
read_dict = {}
count_vectors = {}
for k in read_lengths:
read_dict[k] = []
count_vectors[k] = []
# for each seg, fetch reads, sort them, and create individual count vectors
for seg in cds_part:
reads = gnd.get_reads(seg)
for read in filter(lambda x: len(x.positions) in read_dict,reads):
read_dict[len(read.positions)].append(read)
# map and sort by length
for read_length in read_dict:
count_vector = list(gnd.map_fn(read_dict[read_length],seg)[1])
count_vectors[read_length].extend(count_vector)
# add each count vector for each length to total
for k, vec in count_vectors.items():
counts = numpy.array(vec)
if cds_part.strand == "-":
counts = counts[::-1]
if len(counts) % 3 == 0:
counts = counts.reshape((len(counts)/3,3))
else:
if using_roi == False:
message = "Length of '%s' coding region (%s nt) is not divisible by 3. Ignoring last partial codon." % (roi.get_name(),len(counts))
warnings.warn(message,DataWarning)
newlen = len(counts)//3
counts = counts[:3*newlen]
counts = counts.reshape(newlen,3)
phase_sums[k] += counts[codon_buffer:back_buffer,:].sum(0)
printer.write("Counted %s ROIs total." % (n+1))
for k in dtmp:
dtmp[k] = numpy.array(dtmp[k])
# total reads counted for each size
for k in read_lengths:
dtmp["reads_counted"][dtmp["read_length"] == k] = phase_sums[k].sum()
# read length distribution
dtmp["fraction_reads_counted"] = dtmp["reads_counted"].astype(float) / dtmp["reads_counted"].sum()
# phase vectors
phase_vectors = { K : V.astype(float)/V.astype(float).sum() for K,V in phase_sums.items() }
for i in range(3):
dtmp["phase%s" % i] = numpy.zeros(len(dtmp["read_length"]))
for k, vec in phase_vectors.items():
for i in range(3):
dtmp["phase%s" % i][dtmp["read_length"] == k] = vec[i]
# phase table
fn = "%s_phasing.txt" % args.outbase
printer.write("Saving phasing table to %s ..." % fn)
dtmp = pd.DataFrame(dtmp)
with argsopener(fn,args) as fh:
dtmp.to_csv(fh,columns=["read_length",
"reads_counted",
"fraction_reads_counted",
"phase0",
"phase1",
"phase2",
],
float_format="%.6f",
na_rep="nan",
sep="\t",
index=False,
header=True
)
fh.close()
fig = {}
if args.figsize is not None:
fig["figsize"] = tuple(args.figsize)
colors = pp.get_colors_from_args(args,len(read_lengths))
fn = "%s_phasing.%s" % (args.outbase,args.figformat)
printer.write("Plotting to %s ..." % fn)
plot_counts = numpy.vstack([V for (_,V) in sorted(phase_sums.items())])
fig, (ax1,_) = phase_plot(plot_counts,labels=read_lengths,lighten_by=0.3,
cmap=None,color=colors,fig=fig)
if args.title is not None:
ax1.set_title(args.title)
else:
ax1.set_title("Phasing stats for %s" % args.outbase)
fig.savefig(fn,dpi=args.dpi,bbox_inches="tight")
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:py:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
al = AlignmentParser(
disabled=["normalize", "big_genome", "spliced_bowtie_files"],
input_choices=["BAM"])
an = AnnotationParser()
pp = PlottingParser()
bp = BaseParser()
plotting_parser = pp.get_parser()
alignment_file_parser = al.get_parser(conflict_handler="resolve")
annotation_file_parser = an.get_parser(conflict_handler="resolve")
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
conflict_handler="resolve",
parents=[
base_parser, annotation_file_parser, alignment_file_parser,
plotting_parser
])
parser.add_argument("roi_file",type=str,nargs="?",default=None,
help="Optional. ROI file of maximal spanning windows surrounding start codons, "+\
"from ``metagene generate`` subprogram. Using this instead of `--annotation_files` "+\
"prevents double-counting of codons when multiple transcript isoforms exist "+\
"for a gene. See the documentation for `metagene` for more info about ROI files."+\
"If an ROI file is not given, supply an annotation with ``--annotation_files``")
parser.add_argument("outbase",
type=str,
help="Required. Basename for output files")
parser.add_argument(
"--codon_buffer",
type=int,
default=5,
help="Codons before and after start codon to ignore (Default: 5)")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
pp.set_style_from_args(args)
gnd = al.get_genome_array_from_args(args, printer=printer)
read_lengths = list(range(args.min_length, args.max_length + 1))
codon_buffer = args.codon_buffer
dtmp = {
"read_length": numpy.array(read_lengths),
"reads_counted": numpy.zeros_like(read_lengths, dtype=int),
}
if args.roi_file is not None:
using_roi = True
roi_table = read_pl_table(args.roi_file)
regions = roi_table.iterrows()
transform_fn = roi_row_to_cds
back_buffer = -1
if len(args.annotation_files) > 0:
warnings.warn(
"If an ROI file is given, annotation files are ignored. Pulling regions from '%s'. Ignoring '%s'"
% (args.roi_file, ", ".join(args.annotation_files)),
ArgumentWarning)
else:
using_roi = False
if len(args.annotation_files) == 0:
printer.write(
"Either an ROI file or at least annotation file must be given."
)
sys.exit(1)
else:
warnings.warn(
"Using a transcript annotation file instead of an ROI file can lead to double-counting of codons if the annotation contains multiple transcripts per gene.",
ArgumentWarning)
regions = an.get_transcripts_from_args(args, printer=printer)
back_buffer = -codon_buffer
transform_fn = lambda x: x.get_cds()
phase_sums = {}
for k in read_lengths:
phase_sums[k] = numpy.zeros(3)
for n, roi in enumerate(regions):
if n % 1000 == 1:
printer.write("Counted %s ROIs ..." % n)
# transformation needed to extract CDS from transcript or from ROI file window
cds_part = transform_fn(roi)
# only calculate for coding genes
if len(cds_part) > 0:
read_dict = {}
count_vectors = {}
for k in read_lengths:
read_dict[k] = []
count_vectors[k] = []
# for each seg, fetch reads, sort them, and create individual count vectors
for seg in cds_part:
reads = gnd.get_reads(seg)
for read in filter(lambda x: len(x.positions) in read_dict,
reads):
read_dict[len(read.positions)].append(read)
# map and sort by length
for read_length in read_dict:
count_vector = list(
gnd.map_fn(read_dict[read_length], seg)[1])
count_vectors[read_length].extend(count_vector)
# add each count vector for each length to total
for k, vec in count_vectors.items():
counts = numpy.array(vec)
if cds_part.strand == "-":
counts = counts[::-1]
if len(counts) % 3 == 0:
counts = counts.reshape((int(len(counts) / 3), 3))
else:
if using_roi == False:
message = "Length of '%s' coding region (%s nt) is not divisible by 3. Ignoring last partial codon." % (
roi.get_name(), len(counts))
warnings.warn(message, DataWarning)
newlen = int(len(counts) // 3)
counts = counts[:3 * newlen]
counts = counts.reshape(newlen, 3)
phase_sums[k] += counts[codon_buffer:back_buffer, :].sum(0)
printer.write("Counted %s ROIs total." % (n + 1))
for k in dtmp:
dtmp[k] = numpy.array(dtmp[k])
# total reads counted for each size
for k in read_lengths:
dtmp["reads_counted"][dtmp["read_length"] == k] = phase_sums[k].sum()
# read length distribution
dtmp["fraction_reads_counted"] = dtmp["reads_counted"].astype(
float) / dtmp["reads_counted"].sum()
# phase vectors
phase_vectors = {
K: V.astype(float) / V.astype(float).sum()
for K, V in phase_sums.items()
}
for i in range(3):
dtmp["phase%s" % i] = numpy.zeros(len(dtmp["read_length"]))
for k, vec in phase_vectors.items():
for i in range(3):
dtmp["phase%s" % i][dtmp["read_length"] == k] = vec[i]
# phase table
fn = "%s_phasing.txt" % args.outbase
printer.write("Saving phasing table to %s ..." % fn)
dtmp = pd.DataFrame(dtmp)
with argsopener(fn, args) as fh:
dtmp.to_csv(fh,
columns=[
"read_length",
"reads_counted",
"fraction_reads_counted",
"phase0",
"phase1",
"phase2",
],
float_format="%.6f",
na_rep="nan",
sep="\t",
index=False,
header=True)
fh.close()
fig = {}
if args.figsize is not None:
fig["figsize"] = tuple(args.figsize)
colors = pp.get_colors_from_args(args, len(read_lengths))
fn = "%s_phasing.%s" % (args.outbase, args.figformat)
printer.write("Plotting to %s ..." % fn)
plot_counts = numpy.vstack([V for (_, V) in sorted(phase_sums.items())])
fig, (ax1, _) = phase_plot(plot_counts,
labels=read_lengths,
lighten_by=0.3,
cmap=None,
color=colors,
fig=fig)
if args.title is not None:
ax1.set_title(args.title)
else:
ax1.set_title("Phasing stats for %s" % args.outbase)
fig.savefig(fn, dpi=args.dpi, bbox_inches="tight")
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
al = AlignmentParser(disabled=["normalize"])
an = AnnotationParser()
mp = MaskParser()
pl = PlottingParser()
bp = BaseParser()
alignment_file_parser = al.get_parser()
annotation_file_parser = an.get_parser()
mask_file_parser = mp.get_parser()
plotting_parser = pl.get_parser()
base_parser = bp.get_parser()
generator_help = "Create unambiguous position file from GFF3 annotation"
generator_desc = format_module_docstring(do_generate.__doc__)
counter_help = "Count reads in unambiguous gene positions"
counter_desc = format_module_docstring(do_count.__doc__)
chart_help = "Produce charts comparing reads between samples"
chart_desc = format_module_docstring(do_chart.__doc__)
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter)
subparsers = parser.add_subparsers(
title="subcommands",
description="choose one of the following",
dest="program")
gparser = subparsers.add_parser(
"generate",
help=generator_help,
description=generator_desc,
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[base_parser, annotation_file_parser, mask_file_parser],
)
cparser = subparsers.add_parser(
"count",
help=counter_help,
description=counter_desc,
parents=[base_parser, alignment_file_parser],
formatter_class=argparse.RawDescriptionHelpFormatter,
)
pparser = subparsers.add_parser(
"chart",
help=chart_help,
description=chart_desc,
parents=[base_parser, plotting_parser],
formatter_class=argparse.RawDescriptionHelpFormatter)
gparser.add_argument("outbase",
metavar="outbase",
type=str,
help="Basename for output files")
cparser.add_argument(
"position_file",
type=str,
metavar="file.positions",
help=
"File assigning positions to genes or transcripts (made using 'generate' subcommand)"
)
cparser.add_argument("outbase", type=str, help="Basename for output files")
pparser.add_argument("-i",
"--in",
nargs="+",
type=str,
dest="infiles",
help="input files, made by 'count' subprogram")
pparser.add_argument(
"--bins",
nargs="+",
type=int,
default=(0, 32, 64, 128, 256, 512, 1024, 2048, 4096),
help="Bins into which features are partitioned based on counts")
pparser.add_argument(
"--regions",
nargs="+",
type=str,
default=("exon", "utr5", "cds", "utr3"),
help="Regions to compare (default: exon, utr5, cds, utr3)")
pparser.add_argument("--metrics",
nargs="+",
type=str,
default=("rpkm", "reads"),
help="Metrics to compare (default: rpkm, reads)")
pparser.add_argument(
"list_of_regions",
type=str,
metavar='gene_list.txt',
nargs="?",
default=None,
help=
"Optional. File listing regions (genes or transcripts), one per line, to include in comparisons. If not given, all genes are included."
)
pparser.add_argument("outbase", type=str, help="Basename for output files")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
if args.program == "generate":
#generate position file
do_generate(args, an, mp)
elif args.program == "count":
#use position file to count gene expression in infiles
do_count(args, al)
elif args.program == "chart":
#use count files to generate a family of charts and tables
do_chart(args, pl)
def main(argv=sys.argv[1:]):
"""Command-line program
Parameters
----------
argv : list, optional
A list of command-line arguments, which will be processed
as if the script were called from the command line if
:func:`main` is called directly.
Default: `sys.argv[1:]`. The command-line arguments, if the script is
invoked from the command line
"""
ap = AnnotationParser()
annotation_file_parser = ap.get_parser(conflict_handler="resolve")
al = AlignmentParser(disabled=_DISABLED)
alignment_file_parser = al.get_parser(conflict_handler="resolve")
mp = MaskParser()
mask_file_parser = mp.get_parser()
bp = BaseParser()
base_parser = bp.get_parser()
parser = argparse.ArgumentParser(
description=format_module_docstring(__doc__),
formatter_class=argparse.RawDescriptionHelpFormatter,
parents=[
base_parser, alignment_file_parser, annotation_file_parser,
mask_file_parser
],
)
parser.add_argument("outfile", type=str, help="Output filename")
args = parser.parse_args(argv)
bp.get_base_ops_from_args(args)
ga = al.get_genome_array_from_args(args, printer=printer)
transcripts = ap.get_transcripts_from_args(args,
printer=printer,
return_type=SegmentChain)
crossmap = mp.get_genome_hash_from_args(args, printer=printer)
ga_sum = ga.sum()
normconst = 1000.0 * 1e6 / ga_sum
with argsopener(args.outfile, args, "w") as fout:
fout.write("## total_dataset_counts: %s\n" % ga_sum)
fout.write(
"region_name\tregion\tcounts\tcounts_per_nucleotide\trpkm\tlength\n"
)
for n, ivc in enumerate(transcripts):
name = ivc.get_name()
masks = crossmap.get_overlapping_features(ivc)
ivc.add_masks(*itertools.chain.from_iterable((X for X in masks)))
if n % 1000 == 0:
printer.write("Processed %s regions..." % n)
counts = numpy.nansum(ivc.get_masked_counts(ga))
length = ivc.masked_length
rpnt = numpy.nan if length == 0 else float(counts) / length
rpkm = numpy.nan if length == 0 else rpnt * normconst
ltmp = [
name,
str(ivc),
"%.8e" % counts,
"%.8e" % rpnt,
"%.8e" % rpkm,
"%d" % length
]
fout.write("%s\n" % "\t".join(ltmp))
fout.close()
printer.write("Processed %s regions total." % n)
printer.write("Done.")