Commit cfca8577 authored by Philippe BORDRON's avatar Philippe BORDRON
Browse files

Update according to StringDB changes

parent 0d89f00c
......@@ -305,11 +305,12 @@ for c in conditionVS:
g = dict()
g["category"] = ls[0]
term = ls[1]
id = ls[1].split('.')
id = ls[1].split(':')
category = id[0]
uid = '.'.join(id[1:])
taxa = ls[4]
if g["category"] in ["Component", "Process", "Function"]:
term = '<a href="http://amigo.geneontology.org/amigo/term/GO:{}" target="_blank">{}</a>'.format(uid, term)
term = '<a href="http://amigo.geneontology.org/amigo/term/{}" target="_blank">{}</a>'.format(term, term)
if g["category"] == "InterPro":
term = '<a href="https://www.ebi.ac.uk/interpro/entry/{}" target="_blank">{}</a>'.format(term, term)
if g["category"] == 'KEGG':
......@@ -324,11 +325,13 @@ for c in conditionVS:
term = '<a href="https://reactome.org/content/detail/R-{}" target="_blank">{}</a>'.format(term, term)
if g["category"] == 'SMART':
term = '<a href="http://smart.embl-heidelberg.de/smart/do_annotation.pl?DOMAIN={}" target="_blank">{}</a>'.format(term, term)
if g["category"] == 'NetworkNeighborAL':
term = '<a href="https://string-db.org/cgi/network?network_cluster_id={}&input_query_species={}" target="_blank">{}</a>'.format(term, taxa, term)
g["term"] = term
g["number_of_genes"] = ls[2]
g["number_of_genes_in_background"] = ls[3]
g["gene_ratio"] = str("%.2f" % (int(ls[2]) / int(ls[3])))
g["ncbiTaxonId"] = ls[4]
g["ncbiTaxonId"] = taxa
gc = []
for g1, g2 in zip(ls[5].split(','), ls[6].split(',')):
fc = templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]]["fc"][g1]
......
......@@ -419,7 +419,8 @@
UniProt Keywords (Keyword),
PFAM Protein Domains (Pfam),
INTERPRO Protein Domains and Features (InterPro),
SMART Protein Domains (SMART).
SMART Protein Domains (SMART),
String Local Network Cluster (NetworkNeighborAL).
</p>
{% if stringParams[i.condition1+"__vs__"+i.condition2].counts == 0 %}
......
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