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()
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)