def concatenate_sort_and_index_bams(out_bam, bams):
tmp_bam = out_bam.replace('.bam', '_tmp.bam')
# Drop the UMI tag since it's useless
vdj_utils.concatenate_and_fix_bams(tmp_bam, bams, drop_tags=[PROCESSED_UMI_TAG])
# Wrap filenames in str() to prevent pysam crash on unicode input
tk_bam.sort_and_index(str(tmp_bam), str(out_bam.replace('.bam', '')))
cr_utils.remove(tmp_bam, allow_nonexisting=True)
def rm_files(filenames):
for filename in filenames:
cr_utils.remove(filename, allow_nonexisting=True)
def join(args, outs, chunk_defs, chunk_outs):
contigs = []
contig_fastqs = []
contig_bams = []
if len(chunk_outs) == 0:
# No input reads
# Create empty BAM file
with open(outs.contig_bam, 'w') as f:
pass
outs.contig_bam_bai = None
# Create empty contig FASTA
with open(outs.contig_fasta, 'w') as f:
pass
outs.contig_fasta_fai = None
# Create empty contig FASTQ
with open(outs.contig_fastq, 'w') as f:
pass
outs.metrics_summary_json = None
outs.summary_tsv = None
outs.umi_summary_tsv = None
return
summary_tsvs = []
umi_summary_tsvs = []
for chunk_out in chunk_outs:
if not os.path.isfile(chunk_out.contig_fasta):
continue
contigs.append(chunk_out.contig_fasta)
contig_fastqs.append(chunk_out.contig_fastq)
contig_bams.append(chunk_out.contig_bam)
summary_tsvs.append(chunk_out.summary_tsv)
umi_summary_tsvs.append(chunk_out.umi_summary_tsv)
cr_utils.concatenate_files(outs.contig_fasta, contigs)
if os.path.getsize(outs.contig_fasta) > 0:
tk_subproc.check_call('samtools faidx %s' % outs.contig_fasta,
shell=True)
outs.contig_fasta_fai = outs.contig_fasta + '.fai'
cr_utils.concatenate_files(outs.contig_fastq, contig_fastqs)
if len(summary_tsvs) > 0:
cr_utils.concatenate_headered_files(outs.summary_tsv, summary_tsvs)
if len(umi_summary_tsvs) > 0:
cr_utils.concatenate_headered_files(outs.umi_summary_tsv,
umi_summary_tsvs)
if contig_bams:
# Merge every N BAMs. Trying to merge them all at once
# risks hitting the filehandle limit.
n_merged = 0
while len(contig_bams) > 1:
to_merge = contig_bams[0:MERGE_BAMS_N]
tmp_bam = martian.make_path('merged-%04d.bam' % n_merged)
n_merged += 1
print "Merging %d BAMs into %s ..." % (len(to_merge), tmp_bam)
tk_bam.merge(tmp_bam, to_merge, threads=args.__threads)
# Delete any temporary bams that have been merged
for in_bam in to_merge:
if os.path.basename(in_bam).startswith('merged-'):
cr_utils.remove(in_bam)
# Pop the input bams and push the merged bam
contig_bams = contig_bams[len(to_merge):] + [tmp_bam]
if os.path.basename(contig_bams[0]).startswith('merged-'):
# We merged at least two chunks together.
# Rename it to the output bam.
cr_utils.move(contig_bams[0], outs.contig_bam)
else:
# There was only a single chunk, so copy it from the input
cr_utils.copy(contig_bams[0], outs.contig_bam)
tk_bam.index(outs.contig_bam)
# Make sure the Martian out matches the actual index filename
outs.contig_bam_bai = outs.contig_bam + '.bai'
# Merge the assembler summary jsons
merged_summary = cr_utils.merge_jsons_single_level(
[out.metrics_summary_json for out in chunk_outs])
with open(outs.metrics_summary_json, 'w') as f:
json.dump(tk_safe_json.json_sanitize(merged_summary),
f,
indent=4,
sort_keys=True)