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import sys
import pysam
from deeptools.mapReduce import mapReduce
def countReadsInInterval(args):
chrom, start, end, fname, toEOF = args
bam = openBam(fname)
mapped = 0
unmapped = 0
for b in bam.fetch(chrom, start, end):
if chrom == "*":
unmapped += 1
continue
if b.pos < start:
continue
if not b.is_unmapped:
mapped += 1
else:
unmapped += 1
return mapped, unmapped, chrom
def getMappingStats(bam, nThreads):
"""
This is used for CRAM files, since idxstats() and .mapped/.unmapped are meaningless
This requires pysam > 0.13.0
"""
header = [(x, y) for x, y in zip(bam.references, bam.lengths)]
res = mapReduce([bam.filename, False], countReadsInInterval, header, numberOfProcessors=nThreads)
mapped = sum([x[0] for x in res])
unmapped = sum([x[1] for x in res])
stats = {x[0]: [0, 0] for x in header}
for r in res:
stats[r[2]][0] += r[0]
stats[r[2]][1] += r[1]
# We need to count the number of unmapped reads as well
unmapped += bam.count("*")
return mapped, unmapped, stats
def openBam(bamFile, returnStats=False, nThreads=1, minimalDecoding=True):
"""
A wrapper for opening BAM/CRAM files.
bamFile: str
A BAM/CRAM file name
returnStats: bool
Return a tuple of (file_handle, nMappedReads, nUnmappedReads, statsDict).
These additional values are needed by some downstream functions, since one
can't use file_handle.mapped on CRAM files (or idxstats())
nThreads: int
If returnStats is True, number of threads to use for computing statistics
minimalDecoding: Bool
For CRAM files, don't decode the read name, sequence, qual, or auxiliary tag fields (these aren't used by most functions).
Returns either the file handle or a tuple as described in returnStats
"""
format_options = ["required_fields=0x1FF"]
if sys.version_info.major >= 3:
format_options = [b"required_fields=0x1FF"]
if not minimalDecoding:
format_options = None
try:
bam = pysam.Samfile(bamFile, 'rb', format_options=format_options)
except IOError:
sys.exit("The file '{}' does not exist".format(bamFile))
except:
sys.exit("The file '{}' does not have BAM or CRAM format ".format(bamFile))
try:
assert bam.check_index() is not False
except:
sys.exit("'{}' does not appear to have an index. You MUST index the file first!".format(bamFile))
if bam.is_cram and returnStats:
mapped, unmapped, stats = getMappingStats(bam, nThreads)
elif bam.is_bam:
mapped = bam.mapped
unmapped = bam.unmapped
# Make the dictionary to hold the stats
if returnStats:
stats = {chrom.contig: [chrom.mapped, chrom.unmapped] for chrom in bam.get_index_statistics()}
if bam.is_bam or (bam.is_cram and returnStats):
if mapped == 0:
sys.stderr.write("WARNING! '{}' does not have any mapped reads. Please "
"check that the file is properly indexed and "
"that it contains mapped reads.\n".format(bamFile))
if returnStats:
return bam, mapped, unmapped, stats
else:
return bam
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