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]],
