def search(request):
if request.method == 'GET':
seqname = str(request.GET.get('seqname', '')).strip()
line = request.GET.getlist('line', [])
seq = str(request.GET.get('seq', '')).strip()
evalue = request.GET.get('evalue', '')
refacc = str(request.GET.get('refacc', '')).strip()
refdes = str(request.GET.get('refdes', '')).strip()
order = request.GET.get('order', 'seqname')
items_per_page = request.GET.get('items_per_page', 20)
page = int(request.GET.get('page', 1))
if not str(items_per_page).isdigit():
items_per_page = 20
else:
items_per_page = int(items_per_page)
if 'seqname' in request.GET:
is_search = 1
transcript_search_form = forms.TranscriptSearchForm(request.GET)
else:
is_search = 0
transcript_search_form = forms.TranscriptSearchForm()
else:
raise Http404
if page < 1:
page = 1
else:
pass
search_options = []
if seqname:
search_options.append(Q(seqname__icontains=seqname))
if line:
search_options_line = []
for i in line:
search_options_line.append(Q(line=i))
search_options.append(reduce(OR, search_options_line))
else:
# No line is selected, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
if seq:
try:
evalue = float(evalue)
except ValueError:
# Invalid value, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
fi_seq = NamedTemporaryFile(prefix='seq')
fi_seq.write('>query\n{}\n'.format(seq))
fi_seq.flush()
blastdb_path = []
for i in line:
if settings.BLASTDB.get(i):
blastdb_path.append(os.path.join(settings.BLASTDB_ROOT, settings.BLASTDB.get(i)))
if blastdb_path:
hitnames = blast.blastn_and_gethitnames(fi_seq.name, ' '.join(blastdb_path), evalue)
else:
hitnames = []
fi_seq.close()
if hitnames:
search_options_seq = []
for name in hitnames:
search_options_seq.append(Q(seqname=name))
search_options.append(reduce(OR, search_options_seq))
else:
# No hit is found, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
if refacc:
search_options.append(Q(homology__hit_name_id__accession__icontains=refacc))
if refdes:
search_options.append(Q(homology__hit_description__search=refdes))
transcript_set = Transcript.objects.filter(*search_options).order_by(order)
pager = {
'items_per_page': items_per_page,
'previous_page': None,
'next_page': None,
'first_page': 1,
'last_page': None,
'current_page': page
}
search_count = transcript_set.count()
check_total_page = divmod(search_count, items_per_page)
if search_count == 0:
pager['last_page'] = 1
elif check_total_page[1] == 0:
pager['last_page'] = check_total_page[0]
else:
pager['last_page'] = check_total_page[0] + 1
if page > 1:
# Has previous page
pager['previous_page'] = page - 1
else:
pass
if page * items_per_page < search_count:
# Has next page
pager['next_page'] = page + 1
transcript_subset = transcript_set[(page - 1) * pager.get('items_per_page'): page * pager.get('items_per_page')]
else:
# Last page
transcript_subset = transcript_set[(page - 1) * pager.get('items_per_page'): transcript_set.count()]
return render_to_response(
'transcriptome/search.jinja2',
{
'transcript_search_form': transcript_search_form,
'transcript_subset': transcript_subset,
'pager': pager,
'getparam': request.GET,
'line': line,
'search_count': search_count,
'is_search': is_search,
},
context_instance=RequestContext(request))
def export(request):
if request.method == 'POST':
seqname = request.POST.get('seqname', '').strip('/')
line = request.POST.getlist('line', [])
seq = request.POST.get('seq', '').strip('/')
evalue = request.GET.get('evalue', '')
refacc = request.POST.get('refacc', '').strip('/')
refdes = request.POST.get('refdes', '').strip('/')
order = request.POST.get('order', 'seqname').strip('/')
ids = []
for i in request.POST:
if re.search('_export_\d+', i):
ids.append(request.POST.get(i))
else:
pass
if ids:
# Export selected items
transcript_set = Transcript.objects.filter(id__in=ids).order_by(order)
else:
# Export all filterd items
search_options = []
if seqname:
search_options.append(Q(seqname__icontains=seqname))
if line:
search_options_line = []
for i in line:
search_options_line.append(Q(line=i))
search_options.append(reduce(OR, search_options_line))
else:
# No line is selected, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
if seq:
try:
evalue = float(evalue)
except ValueError:
# Invalid value, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
fi_seq = NamedTemporaryFile(prefix='seq')
fi_seq.write('>query\n{}\n'.format(seq))
fi_seq.flush()
blastdb_path = []
for i in line:
if settings.BLASTDB.get(i):
blastdb_path.append(os.path.join(settings.BLASTDB_ROOT, settings.BLASTDB.get(i)))
if blastdb_path:
hitnames = blast.blastn_and_gethitnames(fi_seq.name, ' '.join(blastdb_path), evalue)
else:
hitnames = []
fi_seq.close()
if hitnames:
search_options_seq = []
for name in hitnames:
search_options_seq.append(Q(seqname=name))
search_options.append(reduce(OR, search_options_seq))
else:
# No hit is found, set id = 0 so fetch 'no result'
search_options.append(Q(id=0))
if refacc:
search_options.append(Q(homology__hit_name_id__accession__icontains=refacc))
if refdes:
search_options.append(Q(homology__hit_description__search=refdes))
else:
pass
transcript_set = Transcript.objects.filter(*search_options).order_by(order)
if request.POST.get('export_fasta'):
# Exports transcript sequences to FASTA file
response = HttpResponse(modelformatter.transcript_to_fasta(transcript_set), content_type='text/csv')
response['Content-Disposition'] = 'attachment; filename=%s' % 'transcript.fa'
return response
elif request.POST.get('export_blast'):
# Exports blast output to TSV format file
response = HttpResponse(modelformatter.transcript_homology_to_blast(transcript_set), content_type='text/csv')
response['Content-Disposition'] = 'attachment; filename=%s' % 'blast.txt'
return response
elif request.POST.get('export_rpkm'):
# Exports rpkm data to TSV format file
response = HttpResponse(modelformatter.transcript_to_expression(transcript_set), content_type='text/csv')
response['Content-Disposition'] = 'attachment; filename=%s' % 'expression.txt'
return response
else:
raise Http404
