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)