def seq_display(request, align_slug):
"""
Serves query display page
:param request: HTTP request
:param align_id: alignment pk
:return:HttpResponse or HttpResponseNotAllowed object
"""
if request.method == 'GET':
# split sequences in chunks of 80 characters
align_id = Alignment.objects.get(slug=align_slug).pk
alignment = consensus_add(Alignment.objects.get_alignment(align_id))
alphabets = {
"Gapped(ExtendedIUPACProtein(), '-')": 'Protein',
"Gapped(ExtendedIUPACDNA(), '-')": 'DNA',
}
alphabet = alphabets[str(alignment[0].seq.alphabet)]
query_seqs = split_lines(alignment, line_length=80, split_type='sequence')
return render(
request,
'base/query_display.html',
{'query_seqs': query_seqs, 'seq_type': alphabet, 'align_id': align_slug}
)
else:
return HttpResponseNotAllowed(['GET'])
def test_split_lines_sequence_splits_lines_of_80_chars(self):
"""
Tests that split_lines function splits sequences in lines of 80 characters by default
"""
alignment = self.alignment
split_sequence = split_lines(alignment, split_type="sequence")
for seq in split_sequence:
self.assertEqual([80 for i in range(len(seq["seq"]) - 1)], [len(s) for s in seq["seq"][:-1]])
self.assertTrue(len(seq["seq"][-1]) <= 80)
def test_split_lines_alignment_splits_blocks_of_80_chars(self):
"""
Tests that split_lines function splits blocks of alignment sequences in lines of 80 characters by default
"""
alignment = self.alignment
split_alignment = split_lines(alignment, split_type="alignment")
for seq in split_alignment[:-1]:
self.assertEqual([80 for i in range(len(seq))], [len(s) for s in seq])
for seq in split_alignment[-1]:
self.assertTrue(len(seq) <= 80)
def align_display(request, align_slug):
"""
serves alignment display page
:param request: HTTP request
:param align_id: alignment pk
:return: HttpResponse object
"""
if request.method == 'GET':
align_id = Alignment.objects.get(slug=align_slug).pk
alignment_fetch = Alignment.objects.get_alignment(align_id)
alignment = consensus_add(alignment_fetch)
alignment = annotate(alignment)
# get longest id for id display width
id_lengths = [len(a.id) for a in alignment]
id_lengths.sort(reverse=True)
id_width = id_lengths[0] + 2
# split sequences in lines of 80 characters
seq_lines = split_lines(alignment, line_length=80, split_type='alignment')
# split lines in blocks of 10 characters
block_length = 10
seqs_blocks = [
[
[
ls.id, [
zip(
ls.letter_annotations['eq'][j:j + block_length],
list(ls[j:j + block_length])
) for j in range(0, len(ls), block_length)
]
] for ls in ln] for ln in seq_lines
]
align = {
'align_seqs': seqs_blocks,
}
r = render(
request, 'base/align_display.html',
{'align': align, 'id_width': id_width * .6, 'total_width': (id_width + 80) * .5}
)
return r
