def flagstats(log, bam):
cmd = [get_user_path("samtools", "samtools"), "flagstat", bam]
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
stdout, stderr = proc.communicate()
result = re.search("(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n(\d+)\s+.*\n", stdout)
result = [int(i) for i in result.groups()]
names = [
"total",
"duplicates",
"mapped",
"paired",
"read1",
"read2",
"properly_paired",
"mate_mapped",
"singletons",
"diff_chromo",
"hq_diff_chromo"
]
result = dict(zip(names, result))
log.info("{},{},{},{},{},{},{}".format(
os.path.basename(bam),
result['total'],
result['duplicates'],
result['mapped'],
round(float(result['mapped'])/result['total'] * 100, 2),
result['mate_mapped'],
round(float(result['mate_mapped'])/result['mapped'] * 100, 2)
))
def faidx(log, fasta):
sample_dir, sample = os.path.split(fasta)
log.info("Indexing FASTA for {}".format(os.path.basename(sample)))
cmd = [get_user_path("samtools", "samtools"), "faidx", fasta]
samtools_fasta_index_out = os.path.join(sample_dir, '{}.samtools-fasta-index.log'.format(sample))
with open(samtools_fasta_index_out, 'w') as samtools_out:
proc = subprocess.Popen(cmd, stdout=samtools_out, stderr=subprocess.STDOUT)
proc.communicate()
def index(log, bam):
sample_dir, sample = os.path.split(bam)
log.info("Indexing BAM for {}".format(os.path.basename(sample)))
cmd = [get_user_path("samtools", "samtools"), "index", bam]
samtools_index_out = os.path.join(sample_dir, '{}.samtools-index.log'.format(sample))
with open(samtools_index_out, 'w') as samtools_out:
proc = subprocess.Popen(cmd, stdout=samtools_out, stderr=subprocess.STDOUT)
proc.communicate()