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create temp files in output directory, not in input dir #7

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29 changes: 15 additions & 14 deletions BAMboozle/BAMboozle.py
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Original file line number Diff line number Diff line change
Expand Up @@ -50,11 +50,11 @@ def idx_bam(bam, threads):
pysam.index(bam)
return bam

def collect_bam_chunks(inpath, chrs, outpath, unmapped):
allpaths = [inpath+".tmp."+c+".bam" for c in chrs]
def collect_bam_chunks(tmppath, chrs, outpath, unmapped):
allpaths = [tmppath+".tmp."+c+".bam" for c in chrs]
if unmapped:
allpaths = [inpath+".tmp."+c+".bam" for c in chrs[:-1]]
allpaths.append(inpath+".tmp."+"unmapped"+".bam")
allpaths = [tmppath+".tmp."+c+".bam" for c in chrs[:-1]]
allpaths.append(tmppath+".tmp."+"unmapped"+".bam")
cat_args = ['-o', outpath]+allpaths
pysam.cat(*cat_args)
x = [os.remove(f) for f in allpaths]
Expand All @@ -73,7 +73,7 @@ def count_ref_consuming_bases(cigartuples):
bases = bases+cig[1]
return bases

def clean_bam(inpath, threads, fastapath, chr, strict, keepunmapped, keepsecondary, anonheader):
def clean_bam(inpath, tmppath, threads, fastapath, chr, strict, keepunmapped, keepsecondary, anonheader):
fa = pysam.FastaFile(fastapath)

if chr == '*':
Expand All @@ -82,10 +82,10 @@ def clean_bam(inpath, threads, fastapath, chr, strict, keepunmapped, keepseconda
chrlabel = chr

#open in/out files
outpath = inpath+".tmp."+chrlabel+".bam"
tmppath = inpath+".tmp."+chrlabel+".tmp.bam"
outpath = tmppath+".tmp."+chrlabel+".bam"
tmppath2 = tmppath+".tmp."+chrlabel+".tmp.bam"
inp = pysam.AlignmentFile(inpath, 'rb', threads = threads)
out = pysam.AlignmentFile(tmppath, 'wb', header = anonheader, threads = threads)
out = pysam.AlignmentFile(tmppath2, 'wb', header = anonheader, threads = threads)
for read in inp.fetch(chr):
# deal with unmapped reads
if chrlabel == 'unmapped':
Expand Down Expand Up @@ -223,11 +223,11 @@ def clean_bam(inpath, threads, fastapath, chr, strict, keepunmapped, keepseconda
except NameError:
readtype = 'NA'
if readtype == 'SE':
pysam.sort("-o", outpath, tmppath)
if os.path.exists(tmppath):
os.remove(tmppath)
pysam.sort("-o", outpath, tmppath2)
if os.path.exists(tmppath2):
os.remove(tmppath2)
else:
os.rename(tmppath, outpath)
os.rename(tmppath2, outpath)


def main():
Expand All @@ -252,6 +252,7 @@ def main():
v = '0.5.0'
print("BAMboozle.py v"+v)
bampath = args.bam
tmppath = args.out + '.tmp'
try:
fa = pysam.FastaFile(args.fa)
except ValueError:
Expand Down Expand Up @@ -282,13 +283,13 @@ def main():
n_jobs = args.p

pool = mp.Pool(n_jobs)
results = [pool.apply_async(clean_bam, (args.bam,pysam_workers,args.fa,chr,args.strict,args.keepunmapped,args.keepsecondary,bamheader, )) for chr in chrs]
results = [pool.apply_async(clean_bam, (args.bam, tmppath,pysam_workers,args.fa,chr,args.strict,args.keepunmapped,args.keepsecondary,bamheader, )) for chr in chrs]
x = [r.get() for r in results]
#single threaded below:
#[clean_bam(bampath,pysam_workers,args.fa,chr,args.strict) for chr in chrs]

print("Creating final output .bam file...")
collect_bam_chunks(inpath = bampath, chrs = chrs, outpath = args.out, unmapped = args.keepunmapped)
collect_bam_chunks(tmppath = tmppath, chrs = chrs, outpath = args.out, unmapped = args.keepunmapped)
print("Indexing final output .bam file...")
y = idx_bam(args.out,args.p)

Expand Down