import os
try:
from config import fastp,tsv2xls
except:
fastp = "fastp"
tsv2xls = "tsv2xls"
from jbiot.logrun import log
sdir = os.path.dirname(os.path.abspath(__file__))
fp2tb = os.path.join(sdir,"fastp2table.py")
[docs]def qc(fqs,prefix):
"""
information for qc
"""
out = "%s.fastp" % prefix
cmd = "mkdir %s" % out
log.info(cmd,prefix)
log.run(cmd,prefix)
log.info("fastq file qc by `fastp`",prefix)
jsons = []
for item in fqs:
fq = item[0]
prex = item[1]
html = prex + ".html"
html = os.path.join(out,html)
json = prex + ".json"
json = os.path.join(out,json)
jsons.append(json)
cmd = "%s -Q -L -i %s -h %s -j %s " % (fastp,fq,html,json)
log.run(cmd,prefix)
jstr = " ".join(jsons)
log.info("convert fastp jsons to table ",prefix)
cmd = "python %s %s %s" % (fp2tb,jstr,prefix)
log.run(cmd,prefix)
tsv = prefix + ".fastqInfo.tsv"
log.info("convert tsv to xls ",prefix)
cmd = "%s %s" % (tsv2xls,tsv)
log.run(cmd,prefix)
return out