if file1name is None:
_print_usage_and_exit(0)
seqs = _read_fasta(file1name)
if len(seqs)==0:
sys.stderr.write("Error: File '"+file1name+"' has no any sequences\n")
sys.exit(5)
name1, seq1 = seqs[0]
if not file2name is None:
seqs = _read_fasta(file2name)
if len(seqs)==0:
sys.stderr.write("Error: File '"+file2name+"' has no any sequences\n")
sys.exit(5)
name2, seq2 = seqs[0]
else:
if len(seqs)<2:
sys.stderr.write("Error: File '"+file1name+"' has only one sequence\n")
sys.exit(6)
name2, seq2 = seqs[1]
matrix = MatrixInfo.__dict__[mn]
sys.stderr.write("Please wait...\n")
als = _base.get_pareto_alignments(seq1,seq2,gep,matrix,40)
primary = _util.get_primary_alignments(als)
# TODO find common parts
cps = None
out.write("# Alignments by PARCA of '"+name1+"' and '"+name2+"'\n")
for pa in primary:
out.write("\n# Score = %i, Deletions = %i, Gaps = %i \n" % (pa.m, pa.d, pa.g))
s = _util.alignment_to_string(seq1,seq2,pa.data,cps,matrix,60)
out.write(s+"\n")
out.close()
for item in test_items:
try:
bioformats.read_sequences_from_file(RESOURCE_PATH+"/test02/in/"+item)
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(
