def implement_cnv(chromosome_event):
chr, event = chromosome_event.split("_")
logger.debug("___ Bamgineer main engine started ___")
success = True
try:
if not terminating.is_set():
bamfn, sortbyname, sortbyCoord, bedfn = init_file_names(
chr, tmpbams_path, haplotype_path, event)
bamsortfn = sub('.bam$', '.sorted.bam', bamfn)
if (os.path.isfile(bedfn)):
fn = list(csv.reader(open(bedfn, 'rb'), delimiter='\t'))
copy_number = int(fn[0][6])
if (not params.GetXY() or (chr != 'chrX' and chr != 'chrY')):
if (copy_number == 2):
event = 'loh'
elif (copy_number == 3):
event = 'gain'
elif (copy_number > 3):
event = 'amp'
else:
logger.debug("*** handling single sex chromosome for: " +
ntpath.basename(bamsortfn))
if (copy_number == 1):
event = 'loh'
elif (copy_number == 2):
event = 'gain'
elif (copy_number > 2):
event = 'amp'
if (event.startswith('amp') or event.startswith('gain')):
bamrepairedsortfn = sub('.sorted.bam$',
".re_paired.sorted.bam", bamsortfn)
mergedsortfn = sub('.sorted.bam$',
".mutated_merged.sorted.bam",
bamrepairedsortfn)
GAIN_FINAL = "/".join(
[finalbams_path,
str(chr).upper() + '_GAIN.bam'])
if os.path.isfile(bamsortfn):
re_pair_reads(bamsortfn, copy_number)
mutate_reads(bamrepairedsortfn, chr, event)
coverageratio = float(
countReads(mergedsortfn)) / float(
countReads(bamsortfn))
logger.debug("+++ coverage ratio for: " +
ntpath.basename(bamsortfn) + ": " +
str(coverageratio))
if coverageratio < copy_number - 2:
logger.error('not enough reads for ' +
ntpath.basename(bamsortfn))
return
else:
samplerate = float(copy_number - 2) / coverageratio
subsample(mergedsortfn, GAIN_FINAL,
str(samplerate))
elif event == 'loss':
inbam_deletion = "/".join(
[finalbams_path,
str(chr).upper() + '_LOSS.bam'])
if os.path.isfile(bamsortfn):
mutate_reads(bamsortfn, chr, 'loss')
mergedsortfn = sub('.sorted.bam$',
".mutated_merged.sorted.bam",
bamsortfn)
mergedsortsampledfn = sub(
'.sorted.bam$',
".mutated_merged.sampled.sorted.bam", bamsortfn)
ratio_kept = float(countReads(bamsortfn)) / float(
countReads(bamfn))
samplerate = round(0.5 / ratio_kept, 2)
LOSS_FINAL = "/".join(
[finalbams_path,
str(chr).upper() + '_LOSS.bam'])
logger.debug("ratios kept for:" +
ntpath.basename(bamsortfn) + ": " +
str(ratio_kept))
subsample(mergedsortfn, mergedsortsampledfn,
str(samplerate))
bamDiff(sortbyCoord, mergedsortsampledfn, tmpbams_path)
os.rename(
"/".join(
[tmpbams_path, 'diff_only1_' + chr + '.bam']),
LOSS_FINAL)
elif (not os.path.isfile(inbam_deletion)
and os.path.isfile(sortbyCoord)
): # if it exists from previous runs
os.symlink(sortbyCoord, inbam_deletion)
else:
logger.debug(bedfn + ' does not exist!')
success = False
except (KeyboardInterrupt):
logger.error(
'Exception Crtl+C pressed in the child process in find_roi_bam for chr '
+ chr + event)
terminating.set()
success = False
return
except Exception as e:
logger.exception("Exception in find_roi_bam %s", e)
terminating.set()
success = False
return
if (success):
logger.debug("implement_cnv complete successfully for " + chr + event)
return
def mutate_reads(bamsortfn, chr, event=''):
fn, sortbyname, sortbyCoord, bedfn = init_file_names(
chr, tmpbams_path, haplotype_path, event)
cmd = " ".join(["sort -u", bedfn, "-o", bedfn])
runCommand(cmd)
hetbamfn = sub('.sorted.bam$', ".mutated_het.bam", bamsortfn)
hetbamfnsorted = sub('.sorted.bam$', ".mutated_het.sorted", bamsortfn)
allreadsfn = sub('.sorted.bam$', ".all.reads.bam", bamsortfn)
allreadssortfn = sub('.sorted.bam$', ".all.reads.sorted", bamsortfn)
mergedsortfn = sub('.sorted.bam$', ".mutated_merged.sorted.bam", bamsortfn)
try:
if not terminating.is_set():
if (os.path.isfile(bamsortfn) and os.path.isfile(bedfn)):
samfile = pysam.Samfile(bamsortfn, "rb")
alignmentfile = pysam.AlignmentFile(bamsortfn, "rb")
outbam = pysam.Samfile(hetbamfn, 'wb', template=samfile)
allreads = pysam.Samfile(allreadsfn, 'wb', template=samfile)
bedfile = open(bedfn, 'r')
covpath = "/".join(
[haplotype_path, "written_coverage_het.txt"])
covfile = open(covpath, 'w')
snpratiopath = "/".join([haplotype_path, "het_snp_ratio.txt"])
snpaltratiofile = open(snpratiopath, 'w')
writtenreads = []
num_reads_written = 0
num_total_reads = 0
for bedline in bedfile:
c = bedline.strip().split()
if (len(c) == 7):
chr2 = c[0]
chr = c[0].strip("chr")
start = int(c[1])
end = int(c[2])
refbase = str(c[3])
altbase = str(c[4])
haplotype = str(c[5])
copy_number = int(c[6])
else:
continue
readmappings = alignmentfile.fetch(chr2, start, end)
# sex chromosome
if (params.GetXY() and (chr == 'chrX' or chr == 'chrY')):
haplotype = 'hap1'
print('sex chromosome ' + str(chr))
for shortread in readmappings:
allreads.write(shortread)
num_total_reads += 1
problem_with_read = False
try:
index = shortread.get_reference_positions(
full_length=True).index(start)
tmpread = shortread.query_sequence
qual = shortread.query_qualities
mutated_hap1 = tmpread[:index] + altbase + tmpread[
index + 1:]
mutated_hap2 = tmpread[:index] + refbase + tmpread[
index + 1:]
if (haplotype == "hap1"):
shortread.query_sequence = mutated_hap1
elif (haplotype == "hap2"):
shortread.query_sequence = mutated_hap2
shortread.query_qualities = qual
except Exception as e:
print('Exception! ')
problem_with_read = True
pass
if (not problem_with_read):
outbam.write(shortread)
num_reads_written += 1
outbam.close()
allreads.close()
sortBam(hetbamfn, hetbamfnsorted + '.bam', tmpbams_path)
sortBam(allreadsfn, allreadssortfn + '.bam', tmpbams_path)
os.remove(hetbamfn)
os.remove(allreadsfn)
# ratio of het reads to nonhet reads, we need to adjust the coverage
ratio = float(num_reads_written) / float(num_total_reads)
bamsortfnsampled = sub('.sorted.bam$', ".sampled.nh.bam",
bamsortfn)
subsample(bamsortfn, bamsortfnsampled, str(ratio))
bamDiff(bamsortfnsampled, allreadssortfn + '.bam',
tmpbams_path)
if ("/".join([
tmpbams_path,
'diff_only1_' + os.path.basename(bamsortfnsampled)
])):
merge_bams(
"/".join([
tmpbams_path,
'diff_only1_' + os.path.basename(bamsortfnsampled)
]), hetbamfnsorted + '.bam', mergedsortfn)
os.remove("/".join([
tmpbams_path,
'diff_only1_' + os.path.basename(bamsortfnsampled)
]))
os.remove(bamsortfnsampled)
os.remove(allreadssortfn + '.bam')
os.remove(allreadssortfn + '.bam.bai')
os.remove(hetbamfnsorted + '.bam')
os.remove(hetbamfnsorted + '.bam.bai')
except (KeyboardInterrupt):
logger.error(
'Exception Crtl+C pressed in the child process in mutaute_reads')
terminating.set()
return
except Exception as e:
logger.exception("Exception in mutate_reads %s", e)
terminating.set()
return
return