def Initialize():
header,seq = fasta.load('MHC_hg18.fa')
sixFrameIter = sequence.sixFrameTranslationIter(seq)
writer = fasta.MfaWriter('6frames.fa')
for frame,p in sixFrameIter:
print 'Frame:', frame
writer.write('%s:%i' % (header,frame),p)
writer.close()
sys.exit()
def Initialize():
header, seq = fasta.load('MHC_hg18.fa')
sixFrameIter = sequence.sixFrameTranslationIter(seq)
writer = fasta.MfaWriter('6frames.fa')
for frame, p in sixFrameIter:
print 'Frame:', frame
writer.write('%s:%i' % (header, frame), p)
writer.close()
sys.exit()
"""
import os, sys
import re, copy
import fasta, sequence, hmmer3
seqFilename = sys.argv[1]
header, seq = fasta.load(seqFilename)
header = header.split()[0]
L = len(seq)
pattern = re.compile('\*')
minLen = 10
sixFrameIter = sequence.sixFrameTranslationIter(seq)
writer = fasta.MfaWriter(sys.stdout)
i = 0
for frame, p in sixFrameIter:
print >> sys.stderr, 'Frame:', frame
matchIter = pattern.finditer(p)
match = matchIter.next()
start = match.start()
for match in matchIter:
end = match.start()
orf = p[start + 1:end]
length = len(orf)
if length >= minLen:
gStart, gEnd, strand = hmmer3.convertSixFrameToGenomic(
import os, sys
import re, copy
import fasta, sequence, hmmer3
seqFilename = sys.argv[1]
header,seq = fasta.load(seqFilename)
header = header.split()[0]
L = len(seq)
pattern = re.compile('\*')
minLen = 10
sixFrameIter = sequence.sixFrameTranslationIter(seq)
writer = fasta.MfaWriter(sys.stdout)
i = 0
for frame,p in sixFrameIter:
print >> sys.stderr, 'Frame:', frame
matchIter = pattern.finditer(p)
match = matchIter.next()
start = match.start()
for match in matchIter:
end = match.start()
orf = p[start+1:end]
length = len(orf)
if length>=minLen:
gStart,gEnd,strand = hmmer3.convertSixFrameToGenomic(start+1, end+1, frame, L)
