def __init__(self, filename):
f = open(filename)
self.commandline = re.match(r'Command line: \[([^]]*)',
f.readline()).group(1)
self.hostname = re.match(r'Hostname: \[([^]]*)', f.readline()).group(1)
self.queries = []
while True:
try:
l = f.next()
except StopIteration, si:
break
if not l:
continue
if l.startswith(C4_ALIGNMENT):
f.next() # skip ------
self.queries.append(Query(f))
elif l.startswith('vulgar:'):
self.queries[-1].vulgar = l[7:].strip()
elif l.startswith(START_GFF):
gff = []
l = f.next()
while not l.startswith(END_GFF):
gff.append(l)
l = f.next()
self.queries[-1].gff = parse_gff2(iter(gff))
def __init__(self, filename):
f = open(filename)
self.commandline = re.match(r'Command line: \[([^]]*)',
f.readline()).group(1)
self.hostname = re.match(r'Hostname: \[([^]]*)',
f.readline()).group(1)
self.queries = []
while True:
try:
l = f.next()
except StopIteration, si:
break
if not l:
continue
if l.startswith(C4_ALIGNMENT):
f.next() # skip ------
self.queries.append(Query(f))
elif l.startswith('vulgar:'):
self.queries[-1].vulgar = l[7:].strip()
elif l.startswith(START_GFF):
gff = []
l = f.next()
while not l.startswith(END_GFF):
gff.append(l)
l = f.next()
self.queries[-1].gff = parse_gff2(iter(gff))
def parse_exonerate(filename):
return parse_gff2(exonerate_file(filename))
def parse_exonerate(filename):
return parse_gff2(exonerate_file(filename))
print "Specify either gff2 or gff3 but not both."
sys.exit(1)
if o.fas is None:
print "Specify the fasta database file."
sys.exit(1)
if o.output is None:
o.output = sys.stdout
else:
o.output = file(o.output, "w")
fas = fasta.Fasta()
fas.read_from(o.fas)
if o.gff2:
gff = parse_gff2.parse_gff2(o.gff2)
else:
gff = parse_gff3.parse_gff3(o.gff3)
try:
l = [fasta.Sequence(
g.reference_sequence + ' ' + g.start + ' ' + g.stop
+ ' ' + g.strand,
fas[g.reference_sequence].sequence[int(g.start)
- 1:int(g.stop)])
for g in gff]
print >> o.output, '\n'.join(imap(str, l))
except KeyError, ke:
print "Sequence was not found in fasta file :", str(ke)
sys.exit(1)
if o.fas is None:
print "Specify the fasta database file."
sys.exit(1)
if o.output is None:
o.output = sys.stdout
else:
o.output = file(o.output, "w")
fas = fasta.Fasta()
fas.read_from(o.fas)
if o.gff2:
gff = parse_gff2.parse_gff2(o.gff2)
else:
gff = parse_gff3.parse_gff3(o.gff3)
try:
l = [
fasta.Sequence(
g.reference_sequence + ' ' + g.start + ' ' + g.stop + ' ' +
g.strand, fas[g.reference_sequence].sequence[int(g.start) -
1:int(g.stop)])
for g in gff
]
print >> o.output, '\n'.join(imap(str, l))
except KeyError, ke:
print "Sequence was not found in fasta file :", str(ke)
