Commit e404dd87 authored by Eric CHARPENTIER's avatar Eric CHARPENTIER 🐍
Browse files

Merge branch 'fix-string-report' into 'master'

Update according to StringDB changes

See merge request !34
parents 0d89f00c 85b2036d
......@@ -296,6 +296,10 @@ for c in conditionVS:
# Building functional enrichment table
templateVars["stringParams"][c["condition1"]+"__vs__"+c["condition2"]]["enrich"] = list()
count = 0
# When enchiched gene list contains 1 gene, the inputGenes list is completed by string with some no DE genes
# We must check them
DEgenes = [x["Gene"] for x in templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]]["genes"]]
# Opening of StringDB file
with open(stringFunctionalEnrichmentFile, "r") as f:
f.readline()
......@@ -305,11 +309,12 @@ 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':
......@@ -324,20 +329,26 @@ 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]
if fc < 0:
color = "green"
sign = "+"
elif fc > 0:
color = "red"
sign = "-"
if g1 in DEgenes: # We must check if inputGenes are DE genes
fc = templateVars["deseqres"][c["condition1"]+"__vs__"+c["condition2"]]["fc"][g1]
if fc < 0:
color = "green"
sign = "+"
elif fc > 0:
color = "red"
sign = "-"
else:
color = "grey"
sign = ""
else:
color = "grey"
sign = ""
......
......@@ -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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