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),
)
def details(request, commonset, refacc):
# Check if object existed
search_options = []
if refacc:
search_options.append(Q(accession=refacc))
commonset_option = {
'for': Q(commonmutation__formothion=1),
'fen': Q(commonmutation__fenthion=1),
'met': Q(commonmutation__methomyl=1),
'for_fen': Q(commonmutation__for_fen=1),
'for_met': Q(commonmutation__for_met=1),
'fen_met': Q(commonmutation__fen_met=1),
'for_fen_met': Q(commonmutation__for_fen_met=1),
}
if commonset_option.get(commonset):
search_options.append(commonset_option.get(commonset))
refseqset = Refseq.objects.filter(*search_options)
if refseqset.count() == 0:
raise Http404
else:
raise Http404
# Obtain msapset
msapset = Msap.objects.filter(hit_name=refacc)
alignment_results = {}
msaps = {}
parser_dna = msaparser.Parser()
parser_protein = msaparser.Parser()
for insecticide in commonset.split('_'):
try:
msap = msapset.get(insecticide=insecticide)
except ObjectDoesNotExist:
continue
else:
msaps.update({insecticide: msap})
try:
ss_transcript = Transcript.objects.get(seqname=msap.ss_name_id)
rs_transcript = Transcript.objects.get(seqname=msap.rs_name_id)
rc_transcript = Transcript.objects.get(seqname=msap.rc_name_id)
except ObjectDoesNotExist:
raise Http404
# Executes multiple sequence alignments
alignment_result_dna = NamedTemporaryFile(prefix='clu_')
alignment_result_dna.write(alignment.multiple_dna(*[(ss_transcript.seqname,
int(msap.ss_frame),
ss_transcript.seq),
(rs_transcript.seqname,
int(msap.rs_frame),
rs_transcript.seq),
(rc_transcript.seqname,
int(msap.rc_frame),
rc_transcript.seq)]))
alignment_result_dna.flush()
parser_dna.parse(alignment_result_dna.name, 'n')
alignment_result_dna.close()
alignment_result_protein = NamedTemporaryFile(prefix='clu_')
alignment_result_protein.write(alignment.multiple_protein(*[(ss_transcript.seqname,
int(msap.ss_frame),
ss_transcript.seq),
(rs_transcript.seqname,
int(msap.rs_frame),
rs_transcript.seq),
(rc_transcript.seqname,
int(msap.rc_frame),
rc_transcript.seq)]))
alignment_result_protein.flush()
parser_protein.parse(alignment_result_protein.name, 'a')
alignment_result_protein.close()
alignment_results.update({insecticide: (parser_dna.get_clustal_html(),
parser_protein.get_clustal_html())})
return render_to_response('transcriptome/svdetails.jinja2',
{'msaps': msaps,
'commonset': commonset,
'refacc': refacc,
'refdes': refseqset[0].description,
'alignment_results': alignment_results},
context_instance=RequestContext(request))
