def assess_sample_primers(sample, fqpair, outfiles, primerlist, primerinfo,
args):
outlabel = fastq_file_label(sample, args.outdir)
loglabel = fastq_file_label(sample, args.logdir) if args.logdir \
else outlabel
frag_primer_file = outlabel + ".read2primers.txt"
primer_read_file = outlabel + ".primer2reads.txt"
logfile = loglabel + ".primer_trim.log"
logfh = open(logfile, 'w')
try:
sys.stderr.write(" Creating primer reports for {}\n".format(sample))
logfh.write("Sample {}\n".format(sample))
if have_files([frag_primer_file, primer_read_file],
args.force,
stderr=logfh):
logfh.write(" Already have {} and {}\n".format(
frag_primer_file, primer_read_file))
frag2primers = arrange_by_fragments(fqpair, outfiles, primerinfo,
logfh)
fragcounts = create_fragment_report(fqpair, frag2primers,
frag_primer_file, True, logfh)
primerreads = bin_primer_reads(frag2primers, primerlist, logfh)
(primercounts,
primerkeys) = create_primer_report(primerreads, primerlist,
primer_read_file, logfh, True,
args.debug)
except Exception, e:
e.args += (sample, )
raise
def assess_sample_primers(sample, fqpair, outfiles, primerlist, primerinfo,
args):
outlabel = fastq_file_label(sample, args.outdir)
loglabel = fastq_file_label(sample, args.logdir) if args.logdir \
else outlabel
frag_primer_file = outlabel + ".read2primers.txt"
primer_read_file = outlabel + ".primer2reads.txt"
logfile = loglabel + ".primer_trim.log"
logfh = open(logfile, 'w')
try:
sys.stderr.write(" Creating primer reports for {}\n".format(sample))
logfh.write("Sample {}\n".format(sample))
if have_files([frag_primer_file, primer_read_file], args.force,
stderr=logfh):
logfh.write(" Already have {} and {}\n".format(frag_primer_file,
primer_read_file))
frag2primers = arrange_by_fragments(fqpair, outfiles, primerinfo,
logfh)
fragcounts = create_fragment_report(fqpair, frag2primers,
frag_primer_file, True, logfh)
primerreads = bin_primer_reads(frag2primers, primerlist, logfh)
(primercounts, primerkeys) = create_primer_report(primerreads,
primerlist, primer_read_file, logfh, True, args.debug)
except Exception, e:
e.args += (sample, )
raise
def trim_primers(fqfile, alignout, max_trim_len, primerinfo, outlabel, logfh,
args):
"""Returns trimmed fastq file and file with list of sequence names"""
trimmedfq = outlabel + ".trimmed.fastq"
seqfile = outlabel + ".seqlist.txt"
logfh.write(" Trimming fq: {}\n".format(trimmedfq))
if have_files([trimmedfq, seqfile], args.force, stderr=logfh):
logfh.write(" Already have {}\n".format(trimmedfq))
return (trimmedfq, seqfile)
aligns = parse_alignout(alignout)
seqlist = []
with open(trimmedfq, 'w') as outfq:
inseq = FastQParser(fqfile)
for seqrec in inseq:
seqlist.append(seqrec.id)
if seqrec.id in aligns:
primer = aligns[seqrec.id]['primer']
if primerinfo[primer]['overlap']:
primerend = aligns[seqrec.id]['end'] +\
aligns[seqrec.id]['left']
subrec = seqrec[primerend:]
if args.debug:
logfh.write("{}\tTrimming\t{}\n".format(
primer, seqrec.id))
else:
if args.debug:
logfh.write("{}\tNot trimming\t{}\n".format(
primer, seqrec.id))
subrec = seqrec
else: #trim default max_primer_len+2
subrec = seqrec[max_trim_len:]
outfq.write("{}\n".format(subrec.fastq()))
logfh.write(" Seq list: {}\n".format(seqfile))
if have_file(seqfile, True, stderr=logfh):
logfh.write(" Still have {}\n".format(seqfile))
sys.exit()
with open_file(seqfile, 'w') as ifh:
ifh.write("\n".join(seqlist) + "\n")
return (trimmedfq, seqfile)
def trim_primers(fqfile, alignout, max_trim_len, primerinfo, outlabel, logfh,
args):
"""Returns trimmed fastq file and file with list of sequence names"""
trimmedfq = outlabel + ".trimmed.fastq"
seqfile = outlabel + ".seqlist.txt"
logfh.write(" Trimming fq: {}\n".format(trimmedfq))
if have_files([trimmedfq, seqfile], args.force, stderr=logfh):
logfh.write(" Already have {}\n".format(trimmedfq))
return (trimmedfq, seqfile)
aligns = parse_alignout(alignout)
seqlist = []
with open(trimmedfq, 'w') as outfq:
inseq = FastQParser(fqfile)
for seqrec in inseq:
seqlist.append(seqrec.id)
if seqrec.id in aligns:
primer = aligns[seqrec.id]['primer']
if primerinfo[primer]['overlap']:
primerend = aligns[seqrec.id]['end'] +\
aligns[seqrec.id]['left']
subrec = seqrec[primerend:]
if args.debug:
logfh.write("{}\tTrimming\t{}\n".format(
primer, seqrec.id))
else:
if args.debug:
logfh.write("{}\tNot trimming\t{}\n".format(
primer, seqrec.id))
subrec = seqrec
else: #trim default max_primer_len+2
subrec = seqrec[max_trim_len:]
outfq.write("{}\n".format(subrec.fastq()))
logfh.write(" Seq list: {}\n".format(seqfile))
if have_file(seqfile, True, stderr=logfh):
logfh.write(" Still have {}\n".format(seqfile))
sys.exit()
with open_file(seqfile, 'w') as ifh:
ifh.write("\n".join(seqlist)+"\n")
return (trimmedfq, seqfile)
