def getFastqPath(archive,bam,fqExt,lane=None):
"""
Function : Given an archive path to sequencing and analysis results, and a BAM file, tries to find the path to the FASTQ file used to generate the BAM, using several assumptions.
Args : archive - str. Archive directory path or a archive name (sequencing run name). In the latter case, SequencingRuns.runPaths.getPubDir does the work.
bam - str. Bam file name (w/o directory path)
fqExt - str. File exension used for the FASTQ file (i.e. 'fastq', or 'fq').
Returns : str, or None.
"""
print("Looking for the FASTQ file that corresponds to BAM file {bam}.".format(bam=bam))
if not os.path.dirname(archive):
archive = runPaths.getPubPath(archive)
fastqBasename = bam.rstrip(".gz")
fastqBasename = fastqBasename.rstrip(".bam") + "." + fqExt
fastqPath = os.path.join(archive,fastqBasename)
print("Checking Path: {}".format(fastqPath))
if os.path.exists(fastqPath):
print("Found it.\n")
return fastqPath
fastqPathGz = fastqPath + ".gz"
print("Checking Path: {}".format(fastqPathGz))
if os.path.exists(fastqPathGz):
print("Found it.\n")
return fastqPathGz
fastqPath = os.path.join(archive,lane,fastqBasename)
print("Checking Path: {}".format(fastqPath))
if os.path.exists(fastqPath):
print("Found it.\n")
return fastqPath
fastqPathGz = fastqPath + ".gz"
print("Checking Path: {}".format(fastqPathGz))
if os.path.exists(fastqPathGz):
print("Found it.\n")
return fastqPathGz
else:
print("\n")
return None