def deplete_blastn_paired(infq1, infq2, outfq1, outfq2, refDbs):
tmpfq1_a = mkstempfname('.fastq')
tmpfq1_b = mkstempfname('.fastq')
tmpfq2_b = mkstempfname('.fastq')
tmpfq2_c = mkstempfname('.fastq')
# deplete fq1
deplete_blastn(infq1, tmpfq1_a, refDbs)
# purge fq2 of read pairs lost in fq1
# (this should significantly speed up the second run of deplete_blastn)
read_utils.purge_unmated(tmpfq1_a, infq2, tmpfq1_b, tmpfq2_b)
# deplete fq2
deplete_blastn(tmpfq2_b, tmpfq2_c, refDbs)
# purge fq1 of read pairs lost in fq2
read_utils.purge_unmated(tmpfq1_b, tmpfq2_c, outfq1, outfq2)
def deplete_blastn_paired(infq1, infq2, outfq1, outfq2, refDbs, threads):
'Use blastn to remove reads that match at least one of the databases.'
tmpfq1_a = mkstempfname('.fastq')
tmpfq1_b = mkstempfname('.fastq')
tmpfq2_b = mkstempfname('.fastq')
tmpfq2_c = mkstempfname('.fastq')
# deplete fq1
deplete_blastn(infq1, tmpfq1_a, refDbs)
# purge fq2 of read pairs lost in fq1
# (this should significantly speed up the second run of deplete_blastn)
read_utils.purge_unmated(tmpfq1_a, infq2, tmpfq1_b, tmpfq2_b)
# deplete fq2
deplete_blastn(tmpfq2_b, tmpfq2_c, refDbs, threads)
# purge fq1 of read pairs lost in fq2
read_utils.purge_unmated(tmpfq1_b, tmpfq2_c, outfq1, outfq2)
def deplete_blastn_paired(infq1, infq2, outfq1, outfq2, refDbs, threads):
'Use blastn to remove reads that match at least one of the databases.'
tmpfq1_a = mkstempfname('.fastq')
tmpfq1_b = mkstempfname('.fastq')
tmpfq2_b = mkstempfname('.fastq')
tmpfq2_c = mkstempfname('.fastq')
# deplete fq1
deplete_blastn(infq1, tmpfq1_a, refDbs)
# purge fq2 of read pairs lost in fq1
# (this should significantly speed up the second run of deplete_blastn)
read_utils.purge_unmated(tmpfq1_a, infq2, tmpfq1_b, tmpfq2_b)
# deplete fq2
deplete_blastn(tmpfq2_b, tmpfq2_c, refDbs, threads)
# purge fq1 of read pairs lost in fq2
read_utils.purge_unmated(tmpfq1_b, tmpfq2_c, outfq1, outfq2)
def trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=100000):
''' Take reads through Trimmomatic, Prinseq, and subsampling.
This should probably move over to read_utils or taxon_filter.
'''
# BAM -> fastq
infq = list(map(util.file.mkstempfname, ['.in.1.fastq', '.in.2.fastq']))
tools.picard.SamToFastqTool().execute(inBam, infq[0], infq[1])
# Trimmomatic
trimfq = list(map(util.file.mkstempfname, ['.trim.1.fastq', '.trim.2.fastq']))
taxon_filter.trimmomatic(infq[0], infq[1], trimfq[0], trimfq[1], clipDb)
os.unlink(infq[0])
os.unlink(infq[1])
# Prinseq
rmdupfq = list(map(util.file.mkstempfname, ['.rmdup.1.fastq', '.rmdup.2.fastq']))
read_utils.rmdup_prinseq_fastq(trimfq[0], rmdupfq[0])
read_utils.rmdup_prinseq_fastq(trimfq[1], rmdupfq[1])
os.unlink(trimfq[0])
os.unlink(trimfq[1])
# Purge unmated
purgefq = list(map(util.file.mkstempfname, ['.fix.1.fastq', '.fix.2.fastq']))
read_utils.purge_unmated(rmdupfq[0], rmdupfq[1], purgefq[0], purgefq[1])
os.unlink(rmdupfq[0])
os.unlink(rmdupfq[1])
# Log count
with open(purgefq[0], 'rt') as inf:
n = int(sum(1 for line in inf)/4)
log.info("PRE-SUBSAMPLE COUNT: %s read pairs", n)
# Subsample
subsampfq = list(map(util.file.mkstempfname, ['.subsamp.1.fastq', '.subsamp.2.fastq']))
cmd = [os.path.join(util.file.get_scripts_path(), 'subsampler.py'),
'-n', str(n_reads),
'-mode', 'p',
'-in', purgefq[0], purgefq[1],
'-out', subsampfq[0], subsampfq[1],
]
subprocess.check_call(cmd)
os.unlink(purgefq[0])
os.unlink(purgefq[1])
# Fastq -> BAM
# Note: this destroys RG IDs! We should instead frun the BAM->fastq step in a way
# breaks out the read groups and perform the above steps in a way that preserves
# the RG IDs.
tmp_bam = util.file.mkstempfname('.subsamp.bam')
tmp_header = util.file.mkstempfname('.header.sam')
tools.samtools.SamtoolsTool().dumpHeader(inBam, tmp_header)
if n == 0:
# FastqToSam cannot deal with empty input
# but Picard SamFormatConverter can deal with empty files
opts = ['INPUT='+tmp_header, 'OUTPUT='+outBam, 'VERBOSITY=ERROR']
tools.picard.PicardTools().execute('SamFormatConverter', opts, JVMmemory='50m')
else:
tools.picard.FastqToSamTool().execute(
subsampfq[0], subsampfq[1], 'Dummy', tmp_bam)
tools.samtools.SamtoolsTool().reheader(tmp_bam, tmp_header, outBam)
os.unlink(tmp_bam)
os.unlink(tmp_header)
os.unlink(subsampfq[0])
os.unlink(subsampfq[1])
def trim_rmdup_subsamp_reads(inBam, clipDb, outBam, n_reads=100000):
''' Take reads through Trimmomatic, Prinseq, and subsampling.
This should probably move over to read_utils or taxon_filter.
'''
# BAM -> fastq
infq = list(map(util.file.mkstempfname, ['.in.1.fastq', '.in.2.fastq']))
tools.picard.SamToFastqTool().execute(inBam, infq[0], infq[1])
# Trimmomatic
trimfq = list(
map(util.file.mkstempfname, ['.trim.1.fastq', '.trim.2.fastq']))
taxon_filter.trimmomatic(infq[0], infq[1], trimfq[0], trimfq[1], clipDb)
os.unlink(infq[0])
os.unlink(infq[1])
# Prinseq
rmdupfq = list(
map(util.file.mkstempfname, ['.rmdup.1.fastq', '.rmdup.2.fastq']))
read_utils.rmdup_prinseq_fastq(trimfq[0], rmdupfq[0])
read_utils.rmdup_prinseq_fastq(trimfq[1], rmdupfq[1])
os.unlink(trimfq[0])
os.unlink(trimfq[1])
# Purge unmated
purgefq = list(
map(util.file.mkstempfname, ['.fix.1.fastq', '.fix.2.fastq']))
read_utils.purge_unmated(rmdupfq[0], rmdupfq[1], purgefq[0], purgefq[1])
os.unlink(rmdupfq[0])
os.unlink(rmdupfq[1])
# Log count
with open(purgefq[0], 'rt') as inf:
n = int(sum(1 for line in inf) / 4)
log.info("PRE-SUBSAMPLE COUNT: %s read pairs", n)
# Subsample
subsampfq = list(
map(util.file.mkstempfname, ['.subsamp.1.fastq', '.subsamp.2.fastq']))
cmd = [
os.path.join(util.file.get_scripts_path(), 'subsampler.py'),
'-n',
str(n_reads),
'-mode',
'p',
'-in',
purgefq[0],
purgefq[1],
'-out',
subsampfq[0],
subsampfq[1],
]
subprocess.check_call(cmd)
os.unlink(purgefq[0])
os.unlink(purgefq[1])
# Fastq -> BAM
# Note: this destroys RG IDs! We should instead frun the BAM->fastq step in a way
# breaks out the read groups and perform the above steps in a way that preserves
# the RG IDs.
tmp_bam = util.file.mkstempfname('.subsamp.bam')
tmp_header = util.file.mkstempfname('.header.sam')
tools.samtools.SamtoolsTool().dumpHeader(inBam, tmp_header)
if n == 0:
# FastqToSam cannot deal with empty input
# but Picard SamFormatConverter can deal with empty files
opts = ['INPUT=' + tmp_header, 'OUTPUT=' + outBam, 'VERBOSITY=ERROR']
tools.picard.PicardTools().execute('SamFormatConverter',
opts,
JVMmemory='50m')
else:
tools.picard.FastqToSamTool().execute(subsampfq[0], subsampfq[1],
'Dummy', tmp_bam)
tools.samtools.SamtoolsTool().reheader(tmp_bam, tmp_header, outBam)
os.unlink(tmp_bam)
os.unlink(tmp_header)
os.unlink(subsampfq[0])
os.unlink(subsampfq[1])
