pattern = re.compile('[\*|X{200,}]') minLen = 20 i = 0 writer = fasta.MfaWriter('ORFs.fa') filename = sys.argv[1] header,dna = fasta.load(filename) header = header.strip() orfIter = sequence.extractOrfsIter(dna, minLen=minLen, pattern=pattern) for i,gStart,gEnd,orf in orfIter: h = '%s.%i.%i-%i Length=%i' % (header,i,gStart,gEnd,len(orf)) writer.write(h, orf) fasta.pretty(h, orf) if gStart<gEnd: s = dna[gStart-1:gEnd] print gStart, gEnd, len(s), len(s) % 3==0 print sequence.codons(s, remainder=True) print sequence.translate(s) else: gStart,gEnd = gEnd,gStart s = dna[gStart-1:gEnd] s = sequence.reverseComplement(s) print gStart, gEnd, len(s), len(s) % 3==0 print sequence.codons(s, remainder=True) print sequence.translate(s) print
action="store_true", dest="complement", help="Complement sequence", default=False) parser.add_option( "-b", "--reverseComplement", "--revComp", action="store_true", dest="reverseComplement", help="Reverse complement sequence", default=False) options, args = parser.parse_args(sys.argv) iFilename = args[1] start = int(args[2]) end = int(args[3]) header,seq = fasta.load(iFilename) s = seq[start-1:end] h = '%s %i-%i' % (header,start,end) if options.reverse: s = sequence.reverse(s) h += '(r)' elif options.complement: s = sequence.complement(s) h += '(c)' elif options.reverseComplement: s = sequence.reverse_complement(s) h += '(rc)' fasta.pretty(h, s, width=options.width)
pattern = re.compile('[\*|X{200,}]') minLen = 20 i = 0 writer = fasta.MfaWriter('ORFs.fa') filename = sys.argv[1] header, dna = fasta.load(filename) header = header.strip() orfIter = sequence.extractOrfsIter(dna, minLen=minLen, pattern=pattern) for i, gStart, gEnd, orf in orfIter: h = '%s.%i.%i-%i Length=%i' % (header, i, gStart, gEnd, len(orf)) writer.write(h, orf) fasta.pretty(h, orf) if gStart < gEnd: s = dna[gStart - 1:gEnd] print gStart, gEnd, len(s), len(s) % 3 == 0 print sequence.codons(s, remainder=True) print sequence.translate(s) else: gStart, gEnd = gEnd, gStart s = dna[gStart - 1:gEnd] s = sequence.reverseComplement(s) print gStart, gEnd, len(s), len(s) % 3 == 0 print sequence.codons(s, remainder=True) print sequence.translate(s) print
help="Complement sequence", default=False) parser.add_option("-b", "--reverseComplement", "--revComp", action="store_true", dest="reverseComplement", help="Reverse complement sequence", default=False) options, args = parser.parse_args(sys.argv) iFilename = args[1] start = int(args[2]) end = int(args[3]) header, seq = fasta.load(iFilename) s = seq[start - 1:end] h = '%s %i-%i' % (header, start, end) if options.reverse: s = sequence.reverse(s) h += '(r)' elif options.complement: s = sequence.complement(s) h += '(c)' elif options.reverseComplement: s = sequence.reverse_complement(s) h += '(rc)' fasta.pretty(h, s, width=options.width)