def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = U.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
group = U.OptionGroup(parser, "group-specific options")
group.add_option(
"--group-out",
dest="tsv",
type="string",
help="Outfile name for file mapping read id to read group",
default=None)
group.add_option(
"--output-bam",
dest="output_bam",
action="store_true",
default=False,
help=("output a bam file with read groups tagged using the UG tag"
"[default=%default]"))
group.add_option(
"--output-unmapped",
dest="output_unmapped",
action="store_true",
default=False,
help=("Retain all unmapped reads in output[default=%default]"))
parser.add_option("--umi-group-tag",
dest="umi_group_tag",
type="string",
help="tag for the outputted umi group",
default='BX')
parser.add_option_group(group)
# add common options (-h/--help, ...) and parse command line
(options, args) = U.Start(parser, argv=argv)
U.validateSamOptions(options)
if options.stdin != sys.stdin:
in_name = options.stdin.name
options.stdin.close()
else:
raise ValueError("Input on standard in not currently supported")
if options.stdout != sys.stdout:
if options.no_sort_output:
out_name = options.stdout.name
else:
out_name = U.getTempFilename()
sorted_out_name = options.stdout.name
options.stdout.close()
assert options.output_bam, (
"To output a bam you must include --output-bam option")
else:
if options.no_sort_output:
out_name = "-"
else:
out_name = U.getTempFilename()
sorted_out_name = "-"
if not options.no_sort_output: # need to determine the output format for sort
if options.out_sam:
sort_format = "sam"
else:
sort_format = "bam"
if options.in_sam:
in_mode = "r"
else:
in_mode = "rb"
if options.out_sam:
out_mode = "wh"
else:
out_mode = "wb"
infile = pysam.Samfile(in_name, in_mode)
if options.output_bam:
outfile = pysam.Samfile(out_name, out_mode, template=infile)
else:
outfile = None
if options.tsv:
mapping_outfile = U.openFile(options.tsv, "w")
mapping_outfile.write("%s\n" % "\t".join([
"read_id", "contig", "position", "gene", "umi", "umi_count",
"final_umi", "final_umi_count", "unique_id"
]))
nInput, nOutput, unique_id, input_reads, output_reads = 0, 0, 0, 0, 0
gene_tag = options.gene_tag
metacontig2contig = None
if options.chrom:
inreads = infile.fetch(reference=options.chrom)
else:
if options.per_gene and options.gene_transcript_map:
metacontig2contig = umi_methods.getMetaContig2contig(
infile, options.gene_transcript_map)
metatag = "MC"
inreads = umi_methods.metafetcher(infile, metacontig2contig,
metatag)
gene_tag = metatag
else:
inreads = infile.fetch(until_eof=options.output_unmapped)
bundle_iterator = umi_methods.get_bundles(
options,
all_reads=True,
return_read2=True,
return_unmapped=options.output_unmapped,
metacontig_contig=metacontig2contig)
for bundle, key, status in bundle_iterator(inreads):
# write out read2s and unmapped (if these options are set)
if status == 'single_read':
# bundle is just a single read here
nInput += 1
if outfile:
outfile.write(bundle)
nOutput += 1
continue
umis = bundle.keys()
counts = {umi: bundle[umi]["count"] for umi in umis}
nInput += sum(counts.values())
while nOutput >= output_reads + 10000:
output_reads += 10000
U.info("Written out %i reads" % output_reads)
while nInput >= input_reads + 1000000:
input_reads += 1000000
U.info("Parsed %i input reads" % input_reads)
# set up UMIClusterer functor with methods specific to
# specified options.method
processor = network.UMIClusterer(options.method)
# group the umis
groups = processor(umis, counts, threshold=options.threshold)
for umi_group in groups:
top_umi = umi_group[0]
group_count = sum(counts[umi] for umi in umi_group)
for umi in umi_group:
reads = bundle[umi]['read']
for read in reads:
if outfile:
# Add the 'UG' tag to the read
read.tags += [('UG', unique_id)]
read.tags += [(options.umi_group_tag, top_umi)]
outfile.write(read)
if options.tsv:
if options.per_gene:
gene = read.get_tag(gene_tag)
else:
gene = "NA"
mapping_outfile.write("%s\n" % "\t".join(
map(str,
(read.query_name, read.reference_name,
umi_methods.get_read_position(
read, options.soft_clip_threshold)[1],
gene, umi.decode(), counts[umi],
top_umi.decode(), group_count, unique_id))))
nOutput += 1
unique_id += 1
if outfile:
outfile.close()
if not options.no_sort_output:
# sort the output
pysam.sort("-o", sorted_out_name, "-O", sort_format, out_name)
os.unlink(out_name) # delete the tempfile
if options.tsv:
mapping_outfile.close()
# write footer and output benchmark information.
U.info("Reads: %s" % ", ".join([
"%s: %s" % (x[0], x[1])
for x in bundle_iterator.read_events.most_common()
]))
U.info("Number of reads out: %i, Number of groups: %i" %
(nOutput, unique_id))
U.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = U.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-i",
"--in-sam",
dest="in_sam",
action="store_true",
help="Input file is in sam format [default=%default]",
default=False)
parser.add_option(
"-o",
"--out-sam",
dest="out_sam",
action="store_true",
help="Output alignments in sam format [default=%default]",
default=False)
parser.add_option("--umi-separator",
dest="umi_sep",
type="string",
help="separator between read id and UMI",
default="_")
parser.add_option("--umi-tag",
dest="umi_tag",
type="string",
help="tag containing umi",
default='RX')
parser.add_option("--umi-group-tag",
dest="umi_group_tag",
type="string",
help="tag for the outputted umi group",
default='BX')
parser.add_option("--extract-umi-method",
dest="get_umi_method",
type="choice",
choices=("read_id", "tag"),
default="read_id",
help="where is the read UMI encoded? [default=%default]")
parser.add_option("--subset",
dest="subset",
type="float",
help="Use only a fraction of reads, specified by subset",
default=None)
parser.add_option("--spliced-is-unique",
dest="spliced",
action="store_true",
help="Treat a spliced read as different to an unspliced"
" one [default=%default]",
default=False)
parser.add_option("--soft-clip-threshold",
dest="soft",
type="float",
help="number of bases clipped from 5' end before"
"read is counted as spliced [default=%default]",
default=4)
parser.add_option("--edit-distance-threshold",
dest="threshold",
type="int",
default=1,
help="Edit distance theshold at which to join two UMIs"
"when clustering. [default=%default]")
parser.add_option("--chrom",
dest="chrom",
type="string",
help="Restrict to one chromosome",
default=None)
parser.add_option("--paired",
dest="paired",
action="store_true",
default=False,
help="paired BAM. [default=%default]")
parser.add_option("--method",
dest="method",
type="choice",
choices=("adjacency", "directional", "unique",
"cluster"),
default="directional",
help="method to use for umi deduping [default=%default]")
parser.add_option("--per-contig",
dest="per_contig",
action="store_true",
default=False,
help=("dedup per contig,"
" e.g for transcriptome where contig = gene"))
parser.add_option(
"--whole-contig",
dest="whole_contig",
action="store_true",
default=False,
help=
"Read whole contig before outputting bundles: guarantees that no reads"
"are missed, but increases memory usage")
parser.add_option(
"--read-length",
dest="read_length",
action="store_true",
default=False,
help=("use read length in addition to position and UMI"
"to identify possible duplicates [default=%default]"))
parser.add_option("--mapping-quality",
dest="mapping_quality",
type="int",
help="Minimum mapping quality for a read to be retained"
" [default=%default]",
default=0)
parser.add_option(
"--group-out",
dest="tsv",
type="string",
help="Outfile name for file mapping read id to read group",
default=None)
parser.add_option(
"--output-bam",
dest="output_bam",
action="store_true",
default=False,
help=("output a bam file with read groups tagged using the UG tag"
"[default=%default]"))
# add common options (-h/--help, ...) and parse command line
(options, args) = U.Start(parser, argv=argv)
if options.stdin != sys.stdin:
in_name = options.stdin.name
options.stdin.close()
else:
raise ValueError("Input on standard in not currently supported")
if options.stdout != sys.stdout:
out_name = options.stdout.name
options.stdout.close()
assert options.output_bam, (
"To output a bam you must include --output-bam option")
else:
out_name = "-"
if options.in_sam:
in_mode = "r"
else:
in_mode = "rb"
if options.out_sam:
out_mode = "w"
else:
out_mode = "wb"
infile = pysam.Samfile(in_name, in_mode)
if options.output_bam:
outfile = pysam.Samfile(out_name, out_mode, template=infile)
if options.paired:
outfile = umi_methods.TwoPassPairWriter(infile, outfile, tags=True)
else:
outfile = None
if options.tsv:
mapping_outfile = U.openFile(options.tsv, "w")
mapping_outfile.write(
"read_id\tcontig\tposition\tumi\tumi_count\tfinal_umi\tfinal_umi_count\tunique_id\n"
)
# set the method with which to extract umis from reads
if options.get_umi_method == "read_id":
umi_getter = partial(umi_methods.get_umi_read_id, sep=options.umi_sep)
elif options.get_umi_method == "tag":
umi_getter = partial(umi_methods.get_umi_tag, tag=options.umi_tag)
else:
raise ValueError("Unknown umi extraction method")
nInput, nOutput, unique_id = 0, 0, 0
read_events = collections.Counter()
for bundle, read_events in umi_methods.get_bundles(
infile,
read_events,
ignore_umi=False,
subset=options.subset,
quality_threshold=options.mapping_quality,
paired=options.paired,
chrom=options.chrom,
spliced=options.spliced,
soft_clip_threshold=options.soft,
per_contig=options.per_contig,
whole_contig=options.whole_contig,
read_length=options.read_length,
umi_getter=umi_getter,
all_reads=True):
nInput += sum([bundle[umi]["count"] for umi in bundle])
if nOutput % 10000 == 0:
U.debug("Outputted %i" % nOutput)
if nInput % 1000000 == 0:
U.debug("Read %i input reads" % nInput)
# set up ReadCluster functor with methods specific to
# specified options.method
processor = network.ReadClusterer(options.method)
bundle, groups, counts = processor(bundle=bundle,
threshold=options.threshold,
stats=True,
deduplicate=False)
for umi_group in groups:
top_umi = umi_group[0]
group_count = sum(counts[umi] for umi in umi_group)
for umi in umi_group:
reads = bundle[umi]['read']
for read in reads:
if outfile:
if options.paired:
# if paired, we need to supply the tags to
# add to the paired read
outfile.write(read, unique_id, top_umi)
else:
# Add the 'UG' tag to the read
read.tags += [('UG', unique_id)]
read.tags += [(options.umi_group_tag, top_umi)]
outfile.write(read)
if options.tsv:
mapping_outfile.write("%s\n" % "\t".join(
map(str, (read.query_name, read.reference_name,
umi_methods.get_read_position(
read, options.soft)[1], umi.decode(),
counts[umi], top_umi.decode(),
group_count, unique_id))))
nOutput += 1
unique_id += 1
if outfile:
outfile.close()
if options.tsv:
mapping_outfile.close()
# write footer and output benchmark information.
U.info(
"Reads: %s" %
", ".join(["%s: %s" % (x[0], x[1])
for x in read_events.most_common()]))
U.info("Number of reads out: %i, Number of groups: %i" %
(nOutput, unique_id))
U.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = U.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-i",
"--in-sam",
dest="in_sam",
action="store_true",
help="Input file is in sam format [default=%default]",
default=False)
parser.add_option(
"-o",
"--out-sam",
dest="out_sam",
action="store_true",
help="Output alignments in sam format [default=%default]",
default=False)
parser.add_option("--umi-separator",
dest="umi_sep",
type="string",
help="separator between read id and UMI",
default="_")
parser.add_option("--umi-tag",
dest="umi_tag",
type="string",
help="tag containing umi",
default='RX')
parser.add_option("--umi-group-tag",
dest="umi_group_tag",
type="string",
help="tag for the outputted umi group",
default='BX')
parser.add_option("--extract-umi-method",
dest="get_umi_method",
type="choice",
choices=("read_id", "tag"),
default="read_id",
help="where is the read UMI encoded? [default=%default]")
parser.add_option("--subset",
dest="subset",
type="float",
help="Use only a fraction of reads, specified by subset",
default=None)
parser.add_option("--spliced-is-unique",
dest="spliced",
action="store_true",
help="Treat a spliced read as different to an unspliced"
" one [default=%default]",
default=False)
parser.add_option("--soft-clip-threshold",
dest="soft",
type="float",
help="number of bases clipped from 5' end before"
"read is counted as spliced [default=%default]",
default=4)
parser.add_option("--edit-distance-threshold",
dest="threshold",
type="int",
default=1,
help="Edit distance theshold at which to join two UMIs"
"when clustering. [default=%default]")
parser.add_option("--chrom",
dest="chrom",
type="string",
help="Restrict to one chromosome",
default=None)
parser.add_option("--paired",
dest="paired",
action="store_true",
default=False,
help="paired BAM. [default=%default]")
parser.add_option("--method",
dest="method",
type="choice",
choices=("adjacency", "directional", "unique",
"cluster"),
default="directional",
help="method to use for umi deduping [default=%default]")
parser.add_option("--per-contig",
dest="per_contig",
action="store_true",
default=False,
help=("dedup per contig (field 3 in BAM; RNAME),"
" e.g for transcriptome where contig = gene"))
parser.add_option("--per-gene",
dest="per_gene",
action="store_true",
default=False,
help=("Deduplicate per gene,"
"e.g for transcriptome where contig = transcript"
"must also provide a transript to gene map with"
"--gene-transcript-map [default=%default]"))
parser.add_option("--gene-transcript-map",
dest="gene_transcript_map",
type="string",
help="file mapping transcripts to genes (tab separated)",
default=None)
parser.add_option("--gene-tag",
dest="gene_tag",
type="string",
help=("Deduplicate per gene where gene is"
"defined by this bam tag [default=%default]"),
default=None)
parser.add_option(
"--read-length",
dest="read_length",
action="store_true",
default=False,
help=("use read length in addition to position and UMI"
"to identify possible duplicates [default=%default]"))
parser.add_option("--mapping-quality",
dest="mapping_quality",
type="int",
help="Minimum mapping quality for a read to be retained"
" [default=%default]",
default=0)
parser.add_option(
"--output-unmapped",
dest="output_unmapped",
action="store_true",
default=False,
help=("Retain all unmapped reads in output[default=%default]"))
parser.add_option(
"--group-out",
dest="tsv",
type="string",
help="Outfile name for file mapping read id to read group",
default=None)
parser.add_option(
"--output-bam",
dest="output_bam",
action="store_true",
default=False,
help=("output a bam file with read groups tagged using the UG tag"
"[default=%default]"))
parser.add_option(
"--skip-tags-regex",
dest="skip_regex",
type="string",
help=("Used with --gene-tag. "
"Ignore reads where the gene-tag matches this regex"),
default="^[__|Unassigned]")
# add common options (-h/--help, ...) and parse command line
(options, args) = U.Start(parser, argv=argv)
if options.stdin != sys.stdin:
in_name = options.stdin.name
options.stdin.close()
else:
raise ValueError("Input on standard in not currently supported")
if options.stdout != sys.stdout:
out_name = options.stdout.name
options.stdout.close()
assert options.output_bam, (
"To output a bam you must include --output-bam option")
else:
out_name = "-"
if options.in_sam:
in_mode = "r"
else:
in_mode = "rb"
if options.out_sam:
out_mode = "wh"
else:
out_mode = "wb"
if options.per_gene:
if not options.gene_transcript_map:
raise ValueError(
"--per-gene option requires --gene-transcript-map")
infile = pysam.Samfile(in_name, in_mode)
if options.output_bam:
outfile = pysam.Samfile(out_name, out_mode, template=infile)
else:
outfile = None
if options.tsv:
mapping_outfile = U.openFile(options.tsv, "w")
mapping_outfile.write("%s\n" % "\t".join([
"read_id", "contig", "position", "gene", "umi", "umi_count",
"final_umi", "final_umi_count", "unique_id"
]))
# set the method with which to extract umis from reads
if options.get_umi_method == "read_id":
umi_getter = partial(umi_methods.get_umi_read_id, sep=options.umi_sep)
elif options.get_umi_method == "tag":
umi_getter = partial(umi_methods.get_umi_tag, tag=options.umi_tag)
else:
raise ValueError("Unknown umi extraction method")
nInput, nOutput, unique_id = 0, 0, 0
if options.chrom:
inreads = infile.fetch(reference=options.chrom)
gene_tag = options.gene_tag
else:
if options.per_gene and options.gene_transcript_map:
metacontig2contig = umi_methods.getMetaContig2contig(
infile, options.gene_transcript_map)
metatag = "MC"
inreads = umi_methods.metafetcher(infile, metacontig2contig,
metatag)
gene_tag = metatag
else:
inreads = infile.fetch(until_eof=options.output_unmapped)
gene_tag = options.gene_tag
for bundle, read_events, status in umi_methods.get_bundles(
inreads,
ignore_umi=False,
subset=options.subset,
quality_threshold=options.mapping_quality,
paired=options.paired,
spliced=options.spliced,
soft_clip_threshold=options.soft,
per_contig=options.per_contig,
gene_tag=gene_tag,
skip_regex=options.skip_regex,
read_length=options.read_length,
umi_getter=umi_getter,
all_reads=True,
return_read2=True,
return_unmapped=options.output_unmapped):
# write out read2s and unmapped if option set
if status == 'single_read':
# bundle is just a single read here
outfile.write(bundle)
nInput += 1
nOutput += 1
continue
umis = bundle.keys()
counts = {umi: bundle[umi]["count"] for umi in umis}
nInput += sum(counts.values())
if nOutput % 10000 == 0:
U.debug("Outputted %i" % nOutput)
if nInput % 1000000 == 0:
U.debug("Read %i input reads" % nInput)
# set up UMIClusterer functor with methods specific to
# specified options.method
processor = network.UMIClusterer(options.method)
# group the umis
groups = processor(umis, counts, threshold=options.threshold)
for umi_group in groups:
top_umi = umi_group[0]
group_count = sum(counts[umi] for umi in umi_group)
for umi in umi_group:
reads = bundle[umi]['read']
for read in reads:
if outfile:
# Add the 'UG' tag to the read
read.tags += [('UG', unique_id)]
read.tags += [(options.umi_group_tag, top_umi)]
outfile.write(read)
if options.tsv:
if options.per_gene:
gene = read.get_tag(gene_tag)
else:
gene = "NA"
mapping_outfile.write("%s\n" % "\t".join(
map(str,
(read.query_name, read.reference_name,
umi_methods.get_read_position(
read, options.soft)[1],
gene, umi.decode(), counts[umi],
top_umi.decode(), group_count, unique_id))))
nOutput += 1
unique_id += 1
if outfile:
outfile.close()
if options.tsv:
mapping_outfile.close()
# write footer and output benchmark information.
U.info(
"Reads: %s" %
", ".join(["%s: %s" % (x[0], x[1])
for x in read_events.most_common()]))
U.info("Number of reads out: %i, Number of groups: %i" %
(nOutput, unique_id))
U.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = U.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
group = U.OptionGroup(parser, "group-specific options")
group.add_option("--group-out", dest="tsv", type="string",
help="Outfile name for file mapping read id to read group",
default=None)
group.add_option("--output-bam", dest="output_bam", action="store_true",
default=False,
help=("output a bam file with read groups tagged using the UG tag"
"[default=%default]"))
group.add_option("--output-unmapped", dest="output_unmapped", action="store_true",
default=False,
help=("Retain all unmapped reads in output[default=%default]"))
parser.add_option("--umi-group-tag", dest="umi_group_tag",
type="string", help="tag for the outputted umi group",
default='BX')
parser.add_option_group(group)
# add common options (-h/--help, ...) and parse command line
(options, args) = U.Start(parser, argv=argv)
U.validateSamOptions(options)
if options.stdin != sys.stdin:
in_name = options.stdin.name
options.stdin.close()
else:
raise ValueError("Input on standard in not currently supported")
if options.stdout != sys.stdout:
if options.no_sort_output:
out_name = options.stdout.name
else:
out_name = U.getTempFilename()
sorted_out_name = options.stdout.name
options.stdout.close()
assert options.output_bam, (
"To output a bam you must include --output-bam option")
else:
if options.no_sort_output:
out_name = "-"
else:
out_name = U.getTempFilename()
sorted_out_name = "-"
if not options.no_sort_output: # need to determine the output format for sort
if options.out_sam:
sort_format = "sam"
else:
sort_format = "bam"
if options.in_sam:
in_mode = "r"
else:
in_mode = "rb"
if options.out_sam:
out_mode = "wh"
else:
out_mode = "wb"
infile = pysam.Samfile(in_name, in_mode)
if options.output_bam:
outfile = pysam.Samfile(out_name, out_mode, template=infile)
else:
outfile = None
if options.tsv:
mapping_outfile = U.openFile(options.tsv, "w")
mapping_outfile.write("%s\n" % "\t".join(
["read_id", "contig", "position", "gene", "umi", "umi_count",
"final_umi", "final_umi_count", "unique_id"]))
nInput, nOutput, unique_id, input_reads, output_reads = 0, 0, 0, 0, 0
gene_tag = options.gene_tag
metacontig2contig = None
if options.chrom:
inreads = infile.fetch(reference=options.chrom)
else:
if options.per_gene and options.gene_transcript_map:
metacontig2contig = umi_methods.getMetaContig2contig(
infile, options.gene_transcript_map)
metatag = "MC"
inreads = umi_methods.metafetcher(infile, metacontig2contig, metatag)
gene_tag = metatag
else:
inreads = infile.fetch(until_eof=options.output_unmapped)
bundle_iterator = umi_methods.get_bundles(
options,
all_reads=True,
return_read2=True,
return_unmapped=options.output_unmapped,
metacontig_contig=metacontig2contig)
for bundle, key, status in bundle_iterator(inreads):
# write out read2s and unmapped (if these options are set)
if status == 'single_read':
# bundle is just a single read here
nInput += 1
if outfile:
outfile.write(bundle)
nOutput += 1
continue
umis = bundle.keys()
counts = {umi: bundle[umi]["count"] for umi in umis}
nInput += sum(counts.values())
while nOutput >= output_reads + 10000:
output_reads += 10000
U.info("Written out %i reads" % output_reads)
while nInput >= input_reads + 1000000:
input_reads += 1000000
U.info("Parsed %i input reads" % input_reads)
# set up UMIClusterer functor with methods specific to
# specified options.method
processor = network.UMIClusterer(options.method)
# group the umis
groups = processor(
umis,
counts,
threshold=options.threshold)
for umi_group in groups:
top_umi = umi_group[0]
group_count = sum(counts[umi] for umi in umi_group)
for umi in umi_group:
reads = bundle[umi]['read']
for read in reads:
if outfile:
# Add the 'UG' tag to the read
read.tags += [('UG', unique_id)]
read.tags += [(options.umi_group_tag, top_umi)]
outfile.write(read)
if options.tsv:
if options.per_gene:
gene = read.get_tag(gene_tag)
else:
gene = "NA"
mapping_outfile.write("%s\n" % "\t".join(map(str, (
read.query_name, read.reference_name,
umi_methods.get_read_position(
read, options.soft_clip_threshold)[1],
gene,
umi.decode(),
counts[umi],
top_umi.decode(),
group_count,
unique_id))))
nOutput += 1
unique_id += 1
if outfile:
outfile.close()
if not options.no_sort_output:
# sort the output
pysam.sort("-o", sorted_out_name, "-O", sort_format, out_name)
os.unlink(out_name) # delete the tempfile
if options.tsv:
mapping_outfile.close()
# write footer and output benchmark information.
U.info(
"Reads: %s" % ", ".join(["%s: %s" % (x[0], x[1]) for x in
bundle_iterator.read_events.most_common()]))
U.info("Number of reads out: %i, Number of groups: %i" %
(nOutput, unique_id))
U.Stop()