def sequence(request):
if 'sequence_id' in request.GET:
uniprot, phogs, best_phogs, orthologs, phog_of_ortholog, error = \
getOrthologQuerySet(
request.GET['sequence_id'],
request.GET.get('ortholog_type', OrthologTypes.PHOG_T_Medium),
request.GET.get('threshold', 0.296874),
)
return render_to_response('hpy/sequence.html', {
'phog_rows': [PHOGRow(phog) for phog in best_phogs],
})
return render_to_response('hpy/sequence.html', {})
def orthologs_as_csv(request, sequence_id):
ortholog_type = OrthologTypes.SuperOrtholog
threshold = 0.0
if 'ortholog_type' in request.GET:
ortholog_type_str = request.GET['ortholog_type']
m = gi_re.match(ortholog_type_str)
if m and len(m.group()) == len(ortholog_type_str):
try:
ortholog_type = int(ortholog_type_str)
if ortholog_type < OrthologTypes.SuperOrtholog \
or ortholog_type > OrthologTypes.PHOG_T_Custom:
ortholog_type = OrthologTypes.SuperOrtholog
except ValueError:
ortholog_type = OrthologTypes.SuperOrtholog
if ortholog_type == OrthologTypes.PHOG_T_Custom and \
'threshold' in request.GET:
threshold_str = request.GET['threshold']
m = float_re.search(threshold_str)
if m and len(m.group()) == len(threshold_str):
try:
threshold = float(threshold_str)
if threshold < 0.0:
threshold = 0.0
except ValueError:
threshold = 0.0
(ownUniProt, phogs, best_phogs,
ortholog_set, phog_of_ortholog, error) \
= getOrthologQuerySet(sequence_id, ortholog_type = ortholog_type,
threshold = threshold)
if ortholog_type == OrthologTypes.SuperOrtholog:
suffix = ''
elif ortholog_type == OrthologTypes.PHOG_T_Tight:
suffix = 'TC'
elif ortholog_type == OrthologTypes.PHOG_T_Medium:
suffix = 'TM'
elif ortholog_type == OrthologTypes.PHOG_T_Loose:
suffix = 'TD'
elif ortholog_type == OrthologTypes.PHOG_T_Custom:
suffix = 'T%g' % threshold
filename = "%s-orthologs_%g.csv" % (sequence_id, threshold)
return csv_ortholog_table_response(ortholog_set, error, filename,
includePHOG = True,
ortholog_type = ortholog_type,
threshold = threshold,
phog_of_ortholog = phog_of_ortholog)
def main():
threshold = preset_thresholds[OrthologTypes.PHOG_T_Tight]
ortholog_type = OrthologTypes.PHOG_T_Tight
(ownUniProt, phogs, best_phogs,
orthologs, phog_of_ortholog, error) \
= getOrthologQuerySet('OXYR_HUMAN', ortholog_type, threshold)
print "Got %d tight orthologs" % len(orthologs)
num_queries_for_tight_orthologs = len(connection.queries)
cum_queries_for_tight_orthologs = len(connection.queries)
print "%d queries were made to get tight orthologs" \
% num_queries_for_tight_orthologs
tight_orthologs_time = 0.0
for query in connection.queries:
tight_orthologs_time += float(query['time'])
print "Total time for tight orthologs: %0.3f" % tight_orthologs_time
phog_rows = [
PHOGRow(phog, ortholog_type, threshold) for phog in best_phogs
]
print "Got %d tight PHOGRows" % len(phog_rows)
num_queries_for_tight_phogrows \
= len(connection.queries) - cum_queries_for_tight_orthologs
cum_queries_for_tight_phogrows = len(connection.queries)
print "%d queries were made to get tight PHOGRows" \
% num_queries_for_tight_phogrows
tight_phogrows_time = 0.0
for query in connection.queries[cum_queries_for_tight_orthologs:]:
tight_phogrows_time += float(query['time'])
print "Total time for tight PHOGRows: %0.3f" % tight_phogrows_time
for phog_row in phog_rows:
print phog_row.accession, "%d sequences" \
% phog_row.num_nonredundant_sequences
threshold = 0.1
ortholog_type = OrthologTypes.PHOG_T_Custom
(ownUniProt, phogs, best_phogs,
orthologs, phog_of_ortholog, error) \
= getOrthologQuerySet('OXYR_HUMAN', ortholog_type, threshold)
print "Got %d custom orthologs at threshold 0.1" % len(orthologs)
num_queries_for_custom_orthologs \
= len(connection.queries) - cum_queries_for_tight_phogrows
cum_queries_for_custom_orthologs = len(connection.queries)
print "%d queries were made to get custom orthologs" \
% num_queries_for_custom_orthologs
custom_orthologs_time = 0.0
for query in connection.queries[cum_queries_for_tight_phogrows:]:
custom_orthologs_time += float(query['time'])
print "Total time for custom orthologs: %0.3f" % custom_orthologs_time
phog_rows = [
PHOGRow(phog, ortholog_type, threshold) for phog in best_phogs
]
print "Got %d custom PHOGRows" % len(phog_rows)
num_queries_for_custom_phogrows \
= len(connection.queries) - cum_queries_for_custom_orthologs
cum_queries_for_custom_phogrows = len(connection.queries)
print "%d queries were made to get custom PHOGRows" \
% num_queries_for_custom_phogrows
custom_phogrows_time = 0.0
for query in connection.queries[cum_queries_for_custom_orthologs:]:
custom_phogrows_time += float(query['time'])
print "Total time for custom PHOGRows: %0.3f" % custom_phogrows_time
for phog_row in phog_rows:
print phog_row.accession, "%d sequences" \
% phog_row.num_nonredundant_sequences
threshold = preset_thresholds[OrthologTypes.PHOG_T_Loose]
ortholog_type = OrthologTypes.PHOG_T_Loose
(ownUniProt, phogs, best_phogs,
orthologs, phog_of_ortholog, error) \
= getOrthologQuerySet('OXYR_HUMAN', ortholog_type, threshold)
print "Got %d loose orthologs" % len(orthologs)
num_queries_for_loose_orthologs = \
len(connection.queries) - cum_queries_for_custom_phogrows
cum_queries_for_loose_orthologs = len(connection.queries)
print "%d queries were made to get loose orthologs" \
% num_queries_for_loose_orthologs
loose_orthologs_time = 0.0
for query in connection.queries[cum_queries_for_custom_phogrows:]:
loose_orthologs_time += float(query['time'])
print "Total time for loose orthologs: %0.3f" % loose_orthologs_time
phog_rows = [
PHOGRow(phog, ortholog_type, threshold) for phog in best_phogs
]
print "Got %d loose PHOGRows" % len(phog_rows)
num_queries_for_loose_phogrows \
= len(connection.queries) - cum_queries_for_loose_orthologs
cum_queries_for_loose_phogrows = len(connection.queries)
print "%d queries were made to get loose PHOGRows" \
% num_queries_for_loose_phogrows
loose_phogrows_time = 0.0
for query in connection.queries[cum_queries_for_loose_orthologs:]:
loose_phogrows_time += float(query['time'])
print "Total time for loose PHOGRows: %0.3f" % loose_phogrows_time
for phog_row in phog_rows:
print phog_row.accession, "%d sequences" \
% phog_row.num_nonredundant_sequences
print "Tight ortholog queries: "
print_query_range(0, cum_queries_for_tight_orthologs)
print "Tight PHOGRow queries: "
print_query_range(cum_queries_for_tight_orthologs,
cum_queries_for_tight_phogrows)
print "Custom ortholog queries: "
print_query_range(cum_queries_for_tight_phogrows,
cum_queries_for_custom_orthologs)
print "Custom PHOGRow queries: "
print_query_range(cum_queries_for_custom_orthologs,
cum_queries_for_custom_phogrows)
print "Loose ortholog queries: "
print_query_range(cum_queries_for_custom_phogrows,
cum_queries_for_loose_orthologs)
print "Loose PHOGRow queries: "
print_query_range(cum_queries_for_loose_orthologs,
cum_queries_for_loose_phogrows)
def netscope(request, sequence_id=None):
if 'sequence_id' in request.GET:
putative_sequence_id = request.GET['sequence_id'].rstrip()
m = phog_re.match(putative_sequence_id.upper())
if m and len(m.group()) == len(putative_sequence_id):
redirect_url = "/net/%s" % putative_sequence_id
return HttpResponseRedirect(redirect_url)
#m = scopid_re.match(putative_sequence_id.lower())
#if not m:
# m = bpgid_re.match(putative_sequence_id.lower())
#if m and len(m.group()) == len(putative_sequence_id):
# redirect_url = "/family/%s" % putative_sequence_id
# return HttpResponseRedirect(redirect_url)
context = {'page_title': "PHOG Interactome Viewer"}
context_for_datagrid = {}
#if sequence_id == None and \
# ('sequence_id' not in request.GET or \
# request.GET['sequence_id'] == u'') and \
# 'sequence_fasta' in request.GET and \
# request.GET['sequence_fasta'] != u'':
# m = fasta_re.match(request.GET['sequence_fasta'])
# if m:
# (sequence_id, record) = get_uniprot_id_from_fasta(request.GET['sequence_fasta'])
# sequence_id = None
# if not record is None:
# return approximate_matches(request, record, context)
# else:
# context['fasta_error'] = 'Invalid FASTA sequence'
# else:
# context['fasta_error'] = 'Invalid FASTA sequence'
if sequence_id != None or \
('sequence_id' in request.GET and \
request.GET['sequence_id'] != request.GET['sequence_id'].upper()):
if not sequence_id:
sequence_id = request.GET['sequence_id'].rstrip()
sequence_id = sequence_id.upper().rstrip()
newGET = request.GET.copy()
newGET.update({'sequence_id': sequence_id})
request.GET = newGET
context['sequence_id'] = sequence_id
context_for_datagrid['extra_query'] = "sequence_id=%s&" % sequence_id
form = OrthologForm(request.GET)
form.sequence_id = sequence_id
elif 'sequence_id' in request.GET:
sequence_id = request.GET['sequence_id'].rstrip()
context['sequence_id'] = request.GET['sequence_id']
context_for_datagrid['extra_query'] \
= "sequence_id=%s" % request.GET['sequence_id']
form = OrthologForm(request.GET)
form.sequence_id = request.GET['sequence_id']
else:
form = OrthologForm()
context['form'] = form
if form.is_bound and form.is_valid() and sequence_id != None and \
sequence_id != u'':
if form.non_field_errors():
context['form_error'] = form.non_field_errors().as_text()
else:
# For some reason, ortholog_type comes in as Unicode
try:
ortholog_type = int(form.cleaned_data['ortholog_type'])
except ValueError:
ortholog_type = OrthologTypes.SuperOrtholog
threshold = form.cleaned_data['threshold']
# threshold = preset_thresholds[ortholog_type]
if (OrthologTypes.SuperOrtholog == ortholog_type):
context['threshold_type'] = "Super orthology"
elif (OrthologTypes.PHOG_T_Tight == ortholog_type):
context['threshold_type'] = "Close"
elif (OrthologTypes.PHOG_T_Medium == ortholog_type):
context['threshold_type'] = "Moderate"
elif (OrthologTypes.PHOG_T_Loose == ortholog_type):
context['threshold_type'] = "Distant"
elif (OrthologTypes.PHOG_T_Custom == ortholog_type):
context['threshold_type'] = "Custom"
else:
context['threshold_type'] = "Unknown"
context_for_datagrid['extra_query'] \
= context_for_datagrid['extra_query'] \
+ "&ortholog_type=%d&threshold=%g" % (ortholog_type, threshold)
(ownUniProt, phogs, best_phogs,
orthologs, phog_of_ortholog, error) \
= getOrthologQuerySet(form.cleaned_data['sequence_id'],
ortholog_type, threshold)
if (error != None):
context['db_error'] = error
else:
have_nontrivial_phogs = False
for phog in phogs.all():
if phog.get_num_nonredundant_sequences(ortholog_type,
threshold) >= 2:
have_nontrivial_phogs = True
if not have_nontrivial_phogs:
context['db_error'] = not_in_phog(sequence_id)
return render_to_response('ppi/netscope.html', context)
context['query_description'] = ownUniProt.description
context['query_species'] = ownUniProt.taxon.scientific_name
taxon = ownUniProt.taxon
taxon_id = taxon.id
(edge_list, node_coords, filename, observed_partners, predicted_partners) = \
run_netscope(ownUniProt, taxon, ortholog_type, threshold)
context['edge_list'] = edge_list
context['node_coords'] = node_coords
context['filename'] = filename
context['taxon_scientific'] = taxon.scientific_name
context['taxon_common'] = taxon.common_name
context['query_sequence_id'] = ownUniProt.id
context['threshold'] = threshold
context['ortholog_type'] = ortholog_type
observed_partner_rows = []
for partner in observed_partners:
observed_partner_rows.append(PartnerRow(partner[0], partner[1]))
context['observed_partners'] = observed_partner_rows
predicted_partner_rows = []
for partner in predicted_partners:
predicted_partner_rows.append(PartnerRow(partner))
context['predicted_partners'] = predicted_partner_rows
return render_to_response('ppi/netscope.html', context)
return render_to_response('ppi/netscope.html', context)
def orthologs(request, sequence_id=None):
with_family_type = request.GET.get('with_family_type', False)
for_iframe = request.GET.get('for_iframe', False)
if 'sequence_id' in request.GET:
putative_sequence_id = request.GET['sequence_id'].strip()
m = phog_re.match(putative_sequence_id.upper())
if m and len(m.group()) == len(putative_sequence_id):
redirect_url = "/phog/%s" % putative_sequence_id
return HttpResponseRedirect(redirect_url)
m = scopid_re.match(putative_sequence_id.lower())
if not m:
m = bpgid_re.match(putative_sequence_id.lower())
if m and len(m.group()) == len(putative_sequence_id):
redirect_url = "/family/%s" % putative_sequence_id
return HttpResponseRedirect(redirect_url)
context = {'page_title': "PHOGs: PhyloFacts Orthology Groups"}
context_for_datagrid = {}
if sequence_id == None and \
('sequence_id' not in request.GET or \
request.GET['sequence_id'] == u'') and \
'sequence_fasta' in request.GET and \
request.GET['sequence_fasta'] != u'':
m = fasta_re.match(request.GET['sequence_fasta'])
if m:
(sequence_id, record) = get_uniprot_id_from_fasta(request.GET['sequence_fasta'])
sequence_id = None
if not record is None:
return approximate_matches(request, record, context)
else:
context['fasta_error'] = 'Invalid FASTA sequence'
else:
context['fasta_error'] = 'Invalid FASTA sequence'
if sequence_id != None or \
('sequence_id' in request.GET and \
request.GET['sequence_id'] != request.GET['sequence_id'].upper()):
if not sequence_id:
sequence_id = request.GET['sequence_id'].rstrip()
sequence_id = sequence_id.upper().rstrip()
newGET = request.GET.copy()
newGET.update({'sequence_id': sequence_id})
request.GET = newGET
context['sequence_id'] = sequence_id
context_for_datagrid['extra_query'] = "sequence_id=%s&" % sequence_id
form = OrthologForm(request.GET)
form.sequence_id = sequence_id
elif 'sequence_id' in request.GET:
sequence_id = request.GET['sequence_id'].rstrip()
context['sequence_id'] = request.GET['sequence_id']
context_for_datagrid['extra_query'] \
= "sequence_id=%s" % request.GET['sequence_id']
form = OrthologForm(request.GET)
form.sequence_id = request.GET['sequence_id']
else:
form = OrthologForm()
context['form'] = form
if form.is_bound and form.is_valid() and sequence_id != None and \
sequence_id != u'':
if form.non_field_errors():
context['form_error'] = form.non_field_errors().as_text()
else:
# For some reason, ortholog_type comes in as Unicode
try:
ortholog_type = int(form.cleaned_data['ortholog_type'])
except ValueError:
ortholog_type = OrthologTypes.SuperOrtholog
threshold = form.cleaned_data['threshold']
context_for_datagrid['extra_query'] \
= context_for_datagrid['extra_query'] \
+ "&ortholog_type=%d&threshold=%g" % (ortholog_type, threshold)
if with_family_type:
context_for_datagrid['extra_query'] += '&with_family_type=1'
if for_iframe:
context_for_datagrid['extra_query'] += '&for_iframe=1'
(ownUniProt, phogs, best_phogs,
orthologs, phog_of_ortholog, error) \
= getOrthologQuerySet(form.cleaned_data['sequence_id'],
ortholog_type, threshold)
if (error != None):
context['db_error'] = error
else:
have_nontrivial_phogs = False
for phog in phogs.all():
if phog.get_num_nonredundant_sequences(ortholog_type,
threshold) >= 2:
have_nontrivial_phogs = True
if not have_nontrivial_phogs:
context['db_error'] = not_in_phog(sequence_id)
return render_to_response('phog/orthologs.html', context)
phog_rows = [PHOGRow(phog, ortholog_type, threshold)
for phog in phogs]
context['phogs'] = phog_rows
#context['phogs'] = []
context['query_description'] = ownUniProt.de
context['query_species'] = ownUniProt.taxon.scientific_name
# Determine if the ppi link should be shown and set appropriate
# context variable if it should.
context['show_ppi_link'] = False
# FIXME: 2010/06/13 RSD
# Commenting this out since we currently don't have the PPI data in
# the schema or models in the database, let alone populated.
"""
for ortholog in orthologs:
if bool(ortholog.sequence_header.uniprot.get_interacting_partners()):
context['show_ppi_link'] = True
# context['ortholog_type'] = ortholog_type
context['netscope_url'] = \
ortholog.sequence_header.uniprot.get_netscope_url(ortholog_type, threshold)
break
"""
## @@@ this is not sufficient as the sequence header identifier may differ
## from the sequence id, resulting in no url being stored.
# Put url for the query into a context variable.
# for ortholog in orthologs:
# if sequence_id == ortholog.sequence_header.identifier():
# context['query_url'] = ortholog.sequence_header.get_absolute_url()
n_sequences_of_family = {}
for phog in phogs:
n_sequences = phog.tree.family.canonical_root_node(
).get_num_included_leaves(OrthologTypes.PHOG_T_Custom,
threshold = 10000.0)
n_sequences_of_family[phog.tree.family] = n_sequences
return OrthologDataGrid(request, orthologs,
with_family_type = with_family_type,
uniprot = ownUniProt,
ortholog_type = ortholog_type,
threshold = threshold,
phog_of_ortholog = phog_of_ortholog,
n_sequences_of_family = n_sequences_of_family,
extra_context=context_for_datagrid).render_to_response(
for_iframe and 'phog/orthologs_for_iframe.html' or 'phog/orthologs.html',
context)
return render_to_response('phog/orthologs.html', context)