def run_statements(self, stmnts, **kwargs):
stmnts = [x for x in stmnts if x]
filename, main_statement, post_statement = P.join_statements(
stmnts, infile=None)
stmnt = " ; ".join([x for x in [main_statement, post_statement] if x])
job_threads1, job_threads2 = 1, 1
if "--num_threads" in stmnt:
try:
job_threads1 = max([
int(x) for x in re.search("--num_threads\s*(\d+)",
stmnt).groups()
])
except AttributeError:
pass
if "--num_cpu_threads_per_data" in stmnt:
try:
job_threads2 = max([
int(x) for x in re.search(
"--num_cpu_threads_per_data_thread\s*(\d+)",
stmnt).groups()
])
except AttributeError:
pass
job_threads = max(job_threads1, job_threads2)
return P.run(stmnt, **kwargs)
def pre_process(self, infile, outfile, params):
statements = []
infile = IOTools.snip(infile, ".bam")
tmpdir = P.get_parameters_as_namedtuple().tmpdir
outprefix = os.path.basename(os.path.dirname(outfile))
if params.copy_bam:
statements.append("cp @[email protected] @[email protected]; "
"cp @[email protected] @[email protected]")
if params.split_bam:
statements.append("daisy bam2bam-split-reads "
"-i @[email protected] "
"-o - "
"{params.split_bam} "
"--log={outfile}_split_bam.log "
"2> {outfile}_split_bam.err "
"> @[email protected]; ".format(**locals()))
if params.bam2bam:
statements.append("daisy bam2bam "
"--stdin=@[email protected] "
"{params.bam2bam} "
"--log={outfile}_bam2bam.log "
"2> {outfile}_bam2bam.err "
"> @[email protected]; ".format(**locals()))
if params.region:
statements.append(
"samtools view -b @[email protected] {} > @[email protected]".format(
params.region))
if params.shift_quality:
statements.append("samtools view -h @[email protected] "
"| perl -lane "
"'if(/^@/) {{print; next;}} "
"@qual=split(//, $F[10]); "
"$_=chr(ord($_)+{}) for (@qual); "
"$F[10]=join(\"\",@qual); "
"print join(\"\\t\", @F)' "
"| samtools view -bS > @[email protected]".format(
params.shift_quality))
if is_true(params.remove_chr):
# also substitute chrM to MT.
statements.append("samtools view -h @[email protected] "
"| awk -v OFS='\\t' '"
"$1 == \"@SQ\" "
"{{ gsub(\"chrM\", \"chrMT\", $2); "
" gsub(\"chr\", \"\", $2); print; next }} "
"{{ gsub(\"chrM\", \"chrMT\", $3); "
" gsub(\"chr\", \"\", $3); print; next}} '"
"| samtools view -bS - "
"2> {outfile}_remove_chr.log "
"> @[email protected]; ".format(**locals()))
if not statements:
return infile + ".bam", "", ""
filename, build_statement, cleanup_statement = P.join_statements(
statements, infile)
filename += ".bam"
build_statement += (
"; samtools index {filename} >& {outfile}.index.log".format(
**locals()))
return filename, build_statement, cleanup_statement