def scalpel_indel(pairs, log_dir, config_file, ref_mnt):
(scalpel, bedtools, bed, fasta, cpus, dustmask_flag, dustmask_bed) = parse_config(config_file)
bed = ref_mnt + '/' + bed
fasta = ref_mnt + '/' + fasta
dustmask_bed = ref_mnt + '/' + dustmask_bed
# use get_merged_bams api
sample_list = 'sample_list.txt'
if not os.path.isfile(sample_list):
create_sample_list(pairs)
sys.stderr.write(date_time() + 'Sample pairs list not created - creating one since this is being run likely '
'outside of pipeline')
get_merged_bams(config_file, sample_list)
fh = open(pairs, 'r')
for line in fh:
cur = line.rstrip('\n').split('\t')
loc = log_dir + cur[0] + '.scalpel.log'
tumor_bam = cur[1] + '.merged.final.bam'
normal_bam = cur[2] + '.merged.final.bam'
scalpel_cmd = scalpel + ' --somatic --logs --numprocs ' + cpus + ' --tumor ' + tumor_bam + ' --normal ' \
+ normal_bam + ' --bed ' + bed + ' --ref ' + fasta + ' 2>> ' + loc
sys.stderr.write(date_time() + 'Starting indel calls for ' + cur[0] + '\n')
log(loc, date_time() + 'Starting indel calls for ' + cur[0] + ' with command:\n' + scalpel_cmd + '\n')
check = call(scalpel_cmd, shell=True)
if check != 0:
sys.stderr.write(date_time() + 'Indel calling failed for pair ' + cur[0] + ' with command:\n' +
scalpel_cmd + '\n')
log(loc, date_time() + 'Indel calling complete for pair ' + cur[0] + ' moving output files\n')
mv_cmd = 'mkdir ' + cur[0] + '; mv outdir/main/* ' + cur[0] + '; rm -rf outdir/main;'
log(loc, date_time() + mv_cmd + '\n')
call(mv_cmd, shell=True)
sys.stderr.write(date_time() + 'Completed indel calls for ' + cur[0] + '\n')
if dustmask_flag == 'Y':
log(loc, date_time() + 'Filter dustmask flag given\n')
check = filter_indel(bedtools, dustmask_bed, cur[0])
if check != 0:
sys.stderr.write(date_time() + 'Dustmask failed for ' + cur[0] + '\n')
exit(1)
else:
log(loc, date_time() + 'Dustmask complete for ' + cur[0] + '\n')
fh.close()
sys.stderr.write(date_time() + 'Indel call completed\n')
return 0
def variant_annot_pipe(config_file, sample_pairs, kflag, ref_mnt, wg):
# create eventual output location directories
mk_dir = 'mkdir BAM LOGS ANALYSIS ANNOTATION'
call(mk_dir, shell=True)
(novosort, obj, cont, analysis, annotation, germ_flag, indel_flag, annot_used) = parse_config(config_file)
# create sample list
sample_list = 'sample_list.txt'
fh = open(sample_pairs, 'r')
sl = open(sample_list, 'w')
temp = {}
for line in fh:
cur = line.rstrip('\n').split('\t')
if cur[1] not in temp:
sl.write(cur[1] + '\n')
temp[cur[1]] = 1
if cur[2] not in temp:
sl.write(cur[2] + '\n')
temp[cur[2]] = 1
sl.close()
fh .close()
del temp
# download and merge (if necessary) bam files
temp_list = check_existing_bams(sample_list)
if len(temp_list) > 0:
sys.stderr.write(date_time() + 'Missing files detected, downloading merged bam files\n')
temp_fn = 'temp_samp_list.txt'
temp_fh = open(temp_fn, 'w')
temp_fh.write('\n'.join(temp_list))
temp_fh.close()
miss_list = get_merged_bams(config_file, temp_fn)
if len(miss_list) == 0:
sys.stderr.write(date_time() + 'Merged bam files successfully download\n')
else:
sys.stderr.write(date_time() + 'Some merged bams appear to be missing, trying downloading constituent bams '
'then merging\n')
missing_fn = 'to_merge.txt'
missing_fh = open(missing_fn, 'w')
missing_fh.write('\n'.join(miss_list))
missing_fh.close()
run_novosort(config_file, missing_fn, obj)
else:
sys.stderr.write(date_time() + 'All bams found. Moving on\n')
if kflag == 'y':
# create bam list for ksort
bam_list = 'bam_list.txt'
blist_cmd = 'ls *.merged.final.bam > ' + bam_list
call(blist_cmd, shell=True)
check = ksort(config_file, bam_list, kflag, ref_mnt)
if check == 0:
sys.stderr.write(date_time() + 'Karyotypic reorder of BAM files completed\n')
else:
sys.stderr.write(date_time() + 'Karyotypic reorder of BAM files failed.\n')
exit(1)
# quick check to see if just need to restart pipleine from mutect, or actually get merged bams
check = mutect_pipe(config_file, sample_pairs, ref_mnt)
if check == 0:
sys.stderr.write(date_time() + 'Mutect variant calls successful\n')
else:
sys.stderr.write(date_time() + 'Mutect variant calls failed.\n')
exit(1)
check = mutect_merge_sort(config_file, sample_pairs, ref_mnt)
if check == 0:
sys.stderr.write(date_time() + 'Mutect file merge successful.\n')
else:
sys.stderr.write(date_time() + 'Mutect file merge failed.\n')
# create def to do vep or snpeff mode for annotation
check = scalpel_indel(sample_pairs, 'LOGS/', config_file, ref_mnt)
if check == 0:
sys.stderr.write(date_time() + 'scalpel successful.\n')
else:
sys.stderr.write(date_time() + 'scalpel failed.\n')
exit(1)
if annot_used == 'snpEff':
snpEff(config_file, sample_pairs, ref_mnt, wg)
if annot_used == 'vep':
vep(config_file, sample_pairs, ref_mnt, '.vcf.keep', '.snv.vep.vcf', 'mutect')
vep(config_file, sample_pairs, ref_mnt, '.indel.vcf', '.somatic.indel.vep.vcf', 'scalpel')
if germ_flag == 'Y':
sys.stderr.write(date_time() + 'Germ line call flag indicated\n')
check = platypus_germline(config_file, sample_pairs, 'LOGS/', wg, ref_mnt)
check += annot_platypus(config_file, sample_pairs, ref_mnt)
if check == 0:
sys.stderr.write(date_time() + 'Germ line call complete\n')
else:
sys.stderr.write(date_time() + 'Error during germline calls. Check output\n')
exit(1)
# relocate stuff, then upload
mv_cmds = 'rm -rf outdir; mv *.bai *.bam BAM; mv *.xls *eff* *sift* *vep* ANNOTATION; mv *out* *vcf* ANALYSIS;'
call(mv_cmds, shell=True)
check = upload_variants_to_swift(cont, obj, sample_list, sample_pairs, analysis, annotation, annot_used)
if check == 0:
sys.stderr.write(date_time() + 'Uploading data to swift successful!\n')
else:
sys.stderr.write(date_time() + 'Uploading data to swift failed!\n')
exit(1)
return 0
