if verbose > 1:
        warn("Cross references: (Pep/DNA) sequence names")
        for key in crossref.keys():
            warn(key + " / " + crossref[key])

    # Do the reverse translation
    newdnaseqs, error = revtrans(dnaseqs, pepseqs, crossref, gapin, gapout,
                                 verbose)

    if verbose: warn("#rev-trans DNA entries: " + str(len(newdnaseqs.keys())))

    if (error > 0):
        warn("# errors:" + str(error) + " aborting ...")
        sys.exit(1)

    # Output the result
    try:
        if outfile != "": out_stream = open(outfile, "w")
        else: out_stream = sys.stdout

        mod_seqfiles.writestream(out_stream, newdnaseqs, outform, "N")

    except Exception, msg:
        warn("Failed to write output." + str(msg))
        if outfile: warn("outfile: " + outfile)
        sys.exit(1)


if __name__ == "__main__":
    main()
Exemple #2
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            continue

        if arg == "--allinternal":
            firstIsStart = False
            continue

        if arg == "-mtx":
            mtxfn = argv[0]
            argv = argv[1:]
            continue

        fn = arg

    mtx = mod_translate.parseMatrixFile(mtxfn)
    try:
        seqs = mod_seqfiles.readfileauto(fn)

        newseqs = {}

        if not maxseqs: maxseqs = len(seqs.keys())
        for key in seqs.keys()[0:maxseqs]:
            seq, note = seqs[key]
            newseqs[key] = mod_translate.translate(seq, mtx, firstIsStart,
                                                   readThroughStop), note

        mod_seqfiles.writestream(sys.stdout, newseqs, "fasta", "P")

    except Exception, e:
        sys.stderr.write("Translation error: %s\n" % str(e))
        sys.exit(1)
		warn (str(len(crossref.keys())+" crossreference(s) could be established."))
	
	if verbose > 1:
		warn("Cross references: (Pep/DNA) sequence names")
		for key in crossref.keys():
			warn(key+" / "+crossref[key]) 

	# Do the reverse translation
	newdnaseqs, error = revtrans(dnaseqs,pepseqs,crossref,gapin,gapout,verbose)
	
	if verbose: warn("#rev-trans DNA entries: "+str(len(newdnaseqs.keys())))
	
	if (error > 0):
		warn ("# errors:"+str(error)+" aborting ...")
		sys.exit(1)
		
	# Output the result
	try:
		if outfile != "": out_stream = open(outfile,"w")
		else:             out_stream = sys.stdout
		
		mod_seqfiles.writestream(out_stream,newdnaseqs,outform,"N")
		
	except Exception, msg:
		warn("Failed to write output."+str(msg))
		if outfile: warn("outfile: "+outfile)
		sys.exit(1)
		
if __name__ == "__main__":
	main()
			readThroughStop = True
			continue

		if arg == "--allinternal":
			firstIsStart = False
			continue

		if arg == "-mtx":
			mtxfn = argv[0]
			argv = argv[1:]
			continue

		fn = arg
			
	mtx = mod_translate.parseMatrixFile(mtxfn)
	try:
		seqs = mod_seqfiles.readfileauto(fn)
	
		newseqs = {}
	
		if not maxseqs: maxseqs = len(seqs.keys())
		for key in seqs.keys()[0:maxseqs]:
			seq, note = seqs[key]
			newseqs[key] = mod_translate.translate(seq,mtx,firstIsStart,readThroughStop) , note
		
		mod_seqfiles.writestream(sys.stdout,newseqs,"fasta","P")
		
	except Exception, e:
		sys.stderr.write("Translation error: %s\n" % str(e))
		sys.exit(1)