def test_parse_xmfa(): file = os.path.join(test_dir, 'test.xmfa') print file fh = open(file, 'r') alignments = parse_xmfa(fh) fh.close() assert len(alignments) == 2 assert len(alignments[0]) == 3 assert len(alignments[0][0]) == 12
column_coords = [] # current coordinate position for each seq in alignment
strands = [] # list of strand information for each seq in alignment
names = [] # list of sequence names
for seq in aln:
(start, strand, name) = parse_id(seq.id)
names.append(name)
strands.append(strand)
column_coords.append(start)
for x in range(len(aln[0])):
row_coords = []
slice = aln[:, x]
for y in range(len(slice)):
if slice[y] != '-':
row_coords.append(names[y] + ':' + str(column_coords[y]))
if strands[y] == '+':
column_coords[y] += 1
else:
column_coords[y] -= 1
else:
row_coords.append('-:-')
coord_array.append(row_coords)
return coord_array
if __name__ == "__main__":
fh = open(sys.argv[1], 'r')
for alignment in parse_xmfa(fh):
if len(alignment) < 2:
continue
for row in parse_coords(alignment):
print ", ".join(row)
