for ch in seq1: if not ch in ALPHABET: sys.stderr.write("Error: first sequence contains symbol out of alphabet\n"); sys.exit(8) for ch in seq2: if not ch in ALPHABET: sys.stderr.write("Error: second sequence contains symbol out of alphabet\n"); sys.exit(8) sys.stderr.write("Please wait...\n") als = _base.get_pareto_alignments(seq1,seq2,gep,matrix,40) err = _base.get_last_error() if len(err)>0: sys.stderr.write("Error: "+err+"\n") sys.exit(7) primary = _util.get_primary_alignments(als) gops = _util.calculate_gops(primary) for index, pa in enumerate(primary): #out.write("\n# Score = %i, Deletions = %i, Gaps = %i \n" % (pa.m, pa.d, pa.g)) gop = gops[index] s = bioformats.proteins_alignment_to_string( pa.data, seq1, seq2, name1, name2, outfmt, matrix, mn, gep, gop, rundate,
has_test2_error = False except: has_test2_error = True failed[2] = not has_test2_error if failed[2]: sys.stderr.write("FAILED\n") else: sys.stderr.write("PASSED\n") _ = "Test 4. Build alignments" sys.stderr.write(_+" (please wait, it takes some time)... ") try: matrix = MatrixInfo.blosum62 seq_names = reference.keys() alns = _base.get_pareto_alignments(reference[seq_names[0]], reference[seq_names[1]], 1.0, matrix, 40) err = _base.get_last_error() assert len(err)==0 gops = _util.calculate_gops(alns) except: failed[3] = True if failed[3]: sys.stderr.write("FAILED\n") else: sys.stderr.write("PASSED\n") _ = "Test 5. Check output formats" sys.stderr.write(_+"... ") try: for outfmt in ["CLUSTAL", "FASTA", "FASTQ", "EMBOSS"]: for index, al in enumerate(alns): gop = gops[index] s = bioformats.proteins_alignment_to_string( al.data, reference[seq_names[0]], reference[seq_names[1]],