def details(request, seqname):
try:
transcript = Transcript.objects.get(seqname=seqname)
except ObjectDoesNotExist:
raise Http404
if transcript.homology_set.all().exists():
reference = Refseq.objects.get(accession=transcript.homology_set.all()[0].hit_name_id)
alignment_protein = alignment.pairwise_protein(transcript.seqname,
transcript.seq,
transcript.homology_set.all()[0].query_frame,
reference.accession,
reference.seq,
transcript.homology_set.all()[0].hit_frame)
alignment_protein_html = formatter.clustal_to_html(alignment_protein, 'a')
else:
alignment_protein_html = ''
return render_to_response('transcriptome/details.jinja2',
{'transcript': transcript,
'alignment_protein_html': alignment_protein_html},
context_instance=RequestContext(request))
def search(request):
if request.method == "GET":
line = request.GET.getlist("line", [])
refacc = str(request.GET.get("refacc", "")).strip()
# order = request.GET.get('order', 'seqname')
if request.GET.get("align_selected"):
align_type = "include"
elif request.GET.get("align_unselected"):
align_type = "exclude"
else:
align_type = "all"
if align_type == "include" or align_type == "exclude":
homo_ids = []
for i in request.GET:
if re.search("homo_\d+", i):
homo_ids.append(int(request.GET.get(i)))
if not homo_ids:
# No selected items
align_type = "all"
if "line" in request.GET:
archive_search_form = forms.ArchiveSearchForm(request.GET)
else:
archive_search_form = forms.ArchiveSearchForm()
else:
raise Http404
homology_set = Homology.objects.filter(hit_name_id=refacc).order_by("query_name")
# Store selection information of homology objects
select_status = {}
if homology_set.exists():
refseq = Refseq.objects.get(accession=refacc)
align_dna_set = []
align_protein_set = []
homology_subset = []
align_protein_set.append((refseq.accession, 0, refseq.seq))
for homology in homology_set:
transcript = Transcript.objects.get(seqname=homology.query_name_id)
if transcript.line in line:
homology_subset.append(homology)
if align_type == "include":
if homology.id in homo_ids:
align_dna_set.append((transcript.seqname, homology.query_frame, transcript.seq))
align_protein_set.append((transcript.seqname, homology.query_frame, transcript.seq))
select_status.update({homology.id: 1})
else:
select_status.update({homology.id: 0})
elif align_type == "exclude":
if homology.id not in homo_ids:
align_dna_set.append((transcript.seqname, homology.query_frame, transcript.seq))
align_protein_set.append((transcript.seqname, homology.query_frame, transcript.seq))
select_status.update({homology.id: 1})
else:
select_status.update({homology.id: 0})
else:
align_dna_set.append((transcript.seqname, homology.query_frame, transcript.seq))
align_protein_set.append((transcript.seqname, homology.query_frame, transcript.seq))
select_status.update({homology.id: 1})
if not align_dna_set:
# No matched results
return render_to_response(
"transcriptome/archive.jinja2",
{"archive_search_form": archive_search_form, "params": request.GET},
context_instance=RequestContext(request),
)
else:
# Run multiple sequence alignments
if len(align_dna_set) > 1:
multiple_dna_alignment = alignment.multiple_dna(*align_dna_set)
multiple_dna_alignment_html = formatter.clustal_to_html(multiple_dna_alignment, "n")
else:
multiple_dna_alignment_html = ""
multiple_protein_alignment = alignment.multiple_protein(*align_protein_set)
multiple_protein_alignment_html = formatter.clustal_to_html(multiple_protein_alignment, "a")
return render_to_response(
"transcriptome/archive.jinja2",
{
"archive_search_form": archive_search_form,
"select_status": select_status,
"homology_subset": homology_subset,
"multiple_dna_alignment_html": multiple_dna_alignment_html,
"multiple_protein_alignment_html": multiple_protein_alignment_html,
"params": request.GET,
},
context_instance=RequestContext(request),
)
else:
# No matched results
return render_to_response(
"transcriptome/archive.jinja2",
{"archive_search_form": archive_search_form, "params": request.GET},
context_instance=RequestContext(request),
)
