def main():
parser = argparse.ArgumentParser(
description="Convert a sam file into a psl file")
parser.add_argument('--genome',
help="FASTA input file of reference genome")
parser.add_argument('--get_secondary_alignments',
action='store_true',
help="Report SA:Z secondary alignments as well")
parser.add_argument('--get_alternative_alignments',
action='store_true',
help="Report XA:Z alternative alignments as well")
parser.add_argument(
'--get_all_alignments',
action='store_true',
help="Report SA:Z and XA:Z alternative alignments as well")
parser.add_argument('--give_unique_names',
action='store_true',
help="Output query names will be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument(
'--output_fasta',
help=
"FILENAME to save an outgoing fasta. Only works for primary alignments."
)
group.add_argument(
'--output_fastq',
help=
"FILENAME to save an outgoing fastq. Only works for primary alignments."
)
parser.add_argument('infile', help="FILENAME input file or '-' for STDIN")
parser.add_argument('-o',
'--output',
help="FILENAME for the output, STDOUT if not set.")
args = parser.parse_args()
if (args.output_fasta
or args.output_fastq) and (args.get_secondary_alignments
or args.get_alternative_alignments
or args.get_all_alignments):
sys.stderr.write(
"ERROR, can only output the fastq/fasta if we are doing primary alignments only.\n"
)
sys.exit()
inf = sys.stdin
if args.infile != '-':
inf = open(args.infile)
of = sys.stdout
if args.output:
of = open(args.output, 'w')
spcf = SamBasics.SAMtoPSLconversionFactory()
if args.genome: spcf.set_genome(args.genome)
off = None
if args.output_fasta:
off = open(args.output_fasta, 'w')
if args.output_fastq:
off = open(args.output_fastq, 'w')
z = 0
for line in inf:
line = line.rstrip()
if SamBasics.is_header(line):
spcf.read_header_line(line)
continue
# We have a line to convert
psl = spcf.convert_line(line)
if psl:
pobj = PSL(psl)
z += 1
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
if args.output_fastq or args.output_fasta:
sam = SamBasics.SAM(line)
sequence = sam.value('seq').upper()
quality = sam.value('qual')
if sam.check_flag(16):
sequence = rc(sam.value('seq').upper())
quality = sam.value('qual')[::-1]
if args.output_fasta:
off.write(">" + pobj.value('qName') + "\n" + sequence +
"\n")
elif args.output_fastq:
if len(sequence) == len(quality):
off.write("@" + pobj.value('qName') + "\n" + sequence +
"\n" + "+\n" + quality + "\n")
else:
sys.stderr.write("ERROR: sequence " + sequence +
" length (" + str(len(sequence)) +
") doesnt match quality " + quality +
" length (" + str(len(quality)) +
")\n")
sys.exit()
# Lets look for secondary alignments to convert
if args.get_secondary_alignments or args.get_all_alignments:
secondary_alignments = SamBasics.get_secondary_alignments(
line.rstrip())
for samline in secondary_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
if args.get_alternative_alignments or args.get_all_alignments:
alternative_alignments = SamBasics.get_alternative_alignments(
line.rstrip())
for samline in alternative_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q' + str(z)
of.write(pobj.get_line() + "\n")
inf.close()
of.close()
def main():
parser = argparse.ArgumentParser(description="Convert a sam file into a psl file")
parser.add_argument('--genome',help="FASTA input file of reference genome")
parser.add_argument('--get_secondary_alignments',action='store_true',help="Report SA:Z secondary alignments as well")
parser.add_argument('--get_alternative_alignments',action='store_true',help="Report XA:Z alternative alignments as well")
parser.add_argument('--get_all_alignments',action='store_true',help="Report SA:Z and XA:Z alternative alignments as well")
parser.add_argument('--give_unique_names',action='store_true',help="Output query names will be unique.")
group = parser.add_mutually_exclusive_group()
group.add_argument('--output_fasta',help="FILENAME to save an outgoing fasta. Only works for primary alignments.")
group.add_argument('--output_fastq',help="FILENAME to save an outgoing fastq. Only works for primary alignments.")
parser.add_argument('infile',help="FILENAME input file or '-' for STDIN")
parser.add_argument('-o','--output',help="FILENAME for the output, STDOUT if not set.")
args = parser.parse_args()
if (args.output_fasta or args.output_fastq) and (args.get_secondary_alignments or args.get_alternative_alignments or args.get_all_alignments):
sys.stderr.write("ERROR, can only output the fastq/fasta if we are doing primary alignments only.\n")
sys.exit()
inf = sys.stdin
if args.infile != '-':
inf = open(args.infile)
of = sys.stdout
if args.output:
of = open(args.output,'w')
spcf = SamBasics.SAMtoPSLconversionFactory()
if args.genome: spcf.set_genome(args.genome)
off = None
if args.output_fasta:
off = open(args.output_fasta,'w')
if args.output_fastq:
off = open(args.output_fastq,'w')
z = 0
for line in inf:
line = line.rstrip()
if SamBasics.is_header(line):
spcf.read_header_line(line)
continue
# We have a line to convert
psl = spcf.convert_line(line)
if psl:
pobj = PSL(psl)
z += 1
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
if args.output_fastq or args.output_fasta:
sam = SamBasics.SAM(line)
sequence = sam.value('seq').upper()
quality = sam.value('qual')
if sam.check_flag(16):
sequence = rc(sam.value('seq').upper())
quality = sam.value('qual')[::-1]
if args.output_fasta:
off.write(">"+pobj.value('qName')+"\n"+sequence+"\n")
elif args.output_fastq:
if len(sequence) == len(quality):
off.write("@"+pobj.value('qName')+"\n"+sequence+"\n"+"+\n"+quality+"\n")
else:
sys.stderr.write("ERROR: sequence "+sequence+" length ("+str(len(sequence))+") doesnt match quality "+quality+" length ("+str(len(quality))+")\n")
sys.exit()
# Lets look for secondary alignments to convert
if args.get_secondary_alignments or args.get_all_alignments:
secondary_alignments = SamBasics.get_secondary_alignments(line.rstrip())
for samline in secondary_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
if args.get_alternative_alignments or args.get_all_alignments:
alternative_alignments = SamBasics.get_alternative_alignments(line.rstrip())
for samline in alternative_alignments:
psl = spcf.convert_line(samline)
if psl:
#print "\nsecondary"
#print samline
z += 1
pobj = PSL(psl)
if args.give_unique_names:
pobj.entry['qName'] = 'Q'+str(z)
of.write(pobj.get_line()+"\n")
inf.close()
of.close()
