def main_deplete(args):
''' Run the entire depletion pipeline: bwa, bmtagger, mvicuna, blastn.
'''
assert len(args.bmtaggerDbs) + len(args.blastDbs) + len(args.bwaDbs) > 0
# only RevertSam if inBam is already aligned
# Most of the time the input will be unaligned
# so we can save save time if we can skip RevertSam in the unaligned case
#
# via the SAM/BAM spec, if the file is aligned, an SQ line should be present
# in the header. Using pysam, we can check this if header['SQ'])>0
# https://samtools.github.io/hts-specs/SAMv1.pdf
# if the user has requested a revertBam
with read_utils.revert_bam_if_aligned(
args.inBam,
revert_bam=args.revertBam,
clear_tags=args.clear_tags,
tags_to_clear=args.tags_to_clear,
picardOptions=['MAX_DISCARD_FRACTION=0.5'],
JVMmemory=args.JVMmemory,
sanitize=not args.do_not_sanitize) as bamToDeplete:
multi_db_deplete_bam(bamToDeplete,
args.bwaDbs,
deplete_bwa_bam,
args.bwaBam,
threads=args.threads)
def bmtagger_wrapper(inBam, db, outBam, JVMmemory=None):
return deplete_bmtagger_bam(inBam,
db,
outBam,
srprism_memory=args.srprism_memory,
JVMmemory=JVMmemory)
multi_db_deplete_bam(args.bwaBam,
args.bmtaggerDbs,
bmtagger_wrapper,
args.bmtaggerBam,
JVMmemory=args.JVMmemory)
# if the user has not specified saving a revertBam, we used a temp file and can remove it
if not args.revertBam:
os.unlink(revertBamOut)
read_utils.rmdup_mvicuna_bam(args.bmtaggerBam,
args.rmdupBam,
JVMmemory=args.JVMmemory)
multi_db_deplete_bam(args.rmdupBam,
args.blastDbs,
deplete_blastn_bam,
args.blastnBam,
chunkSize=args.chunkSize,
threads=args.threads,
JVMmemory=args.JVMmemory)
return 0
def main_deplete(args):
''' Run the entire depletion pipeline: bwa, bmtagger, mvicuna, blastn.
'''
assert len(args.bmtaggerDbs) + len(args.blastDbs) + len(args.bwaDbs) > 0
# only RevertSam if inBam is already aligned
# Most of the time the input will be unaligned
# so we can save save time if we can skip RevertSam in the unaligned case
#
# via the SAM/BAM spec, if the file is aligned, an SQ line should be present
# in the header. Using pysam, we can check this if header['SQ'])>0
# https://samtools.github.io/hts-specs/SAMv1.pdf
# if the user has requested a revertBam
with read_utils.revert_bam_if_aligned( args.inBam,
revert_bam = args.revertBam,
clear_tags = args.clear_tags,
tags_to_clear = args.tags_to_clear,
picardOptions = ['MAX_DISCARD_FRACTION=0.5'],
JVMmemory = args.JVMmemory,
sanitize = not args.do_not_sanitize) as bamToDeplete:
multi_db_deplete_bam(
bamToDeplete,
args.bwaDbs,
deplete_bwa_bam,
args.bwaBam,
threads=args.threads
)
def bmtagger_wrapper(inBam, db, outBam, JVMmemory=None):
return deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=args.srprism_memory, JVMmemory=JVMmemory)
multi_db_deplete_bam(
args.bwaBam,
args.bmtaggerDbs,
bmtagger_wrapper,
args.bmtaggerBam,
JVMmemory=args.JVMmemory
)
# if the user has not specified saving a revertBam, we used a temp file and can remove it
if not args.revertBam:
os.unlink(revertBamOut)
read_utils.rmdup_mvicuna_bam(args.bmtaggerBam, args.rmdupBam, JVMmemory=args.JVMmemory)
multi_db_deplete_bam(
args.rmdupBam,
args.blastDbs,
deplete_blastn_bam,
args.blastnBam,
chunkSize=args.chunkSize,
threads=args.threads,
JVMmemory=args.JVMmemory
)
return 0
def main_deplete_bwa_bam(args):
'''Use BWA to remove reads that match at least one of the specified databases.'''
with read_utils.revert_bam_if_aligned( args.inBam,
clear_tags = args.clear_tags,
tags_to_clear = args.tags_to_clear,
picardOptions = ['MAX_DISCARD_FRACTION=0.5'],
JVMmemory = args.JVMmemory,
sanitize = not args.do_not_sanitize) as bamToDeplete:
#def wrapper(inBam, db, outBam, threads, JVMmemory=None):
# return deplete_bwa_bam(inBam, db, outBam, threads=threads, )
multi_db_deplete_bam(bamToDeplete, args.refDbs, deplete_bwa_bam, args.outBam, threads=args.threads, clear_tags=args.clear_tags, tags_to_clear=args.tags_to_clear, JVMmemory=args.JVMmemory)
return 0
def main_deplete_bam_bmtagger(args):
'''Use bmtagger to deplete input reads against several databases.'''
def bmtagger_wrapper(inBam, db, outBam, JVMmemory=None):
return deplete_bmtagger_bam(inBam, db, outBam, srprism_memory=args.srprism_memory, JVMmemory=JVMmemory)
with read_utils.revert_bam_if_aligned( args.inBam,
clear_tags = args.clear_tags,
tags_to_clear = args.tags_to_clear,
picardOptions = ['MAX_DISCARD_FRACTION=0.5'],
JVMmemory = args.JVMmemory,
sanitize = not args.do_not_sanitize) as bamToDeplete:
multi_db_deplete_bam(
args.inBam,
args.refDbs,
bmtagger_wrapper,
args.outBam,
JVMmemory=args.JVMmemory
)