diff options
Diffstat (limited to 'gatpub.py')
| -rwxr-xr-x | gatpub.py | 39 |
1 files changed, 21 insertions, 18 deletions
@@ -39,7 +39,7 @@ def gene_addiction(gene): if findWholeWord(drug_d[drug0])(sent) : sent=re.sub(r'\b(%s)\b' % drug_d[drug0], r'<b>\1</b>', sent, flags=re.I) out+=gene+"\t"+"drug\t" + drug0+"\t"+sent+"\n" - for add0 in addiction.split("|"): + for add0 in addiction_d: if findWholeWord(add0)(sent) : sent=re.sub(r'\b(%s)\b' % add0, r'<b>\1</b>', sent, flags=re.I) out+=gene+"\t"+"addiction\t"+add0+"\t"+sent+"\n" @@ -67,28 +67,37 @@ def gene_functional(gene): out+=gene+"\t"+"function\t"+bio0+"\t"+sent+"\n" return(out) -def generate_nodes(nodes_d): +def generate_nodes(nodes_d, nodecolor): # include all search terms even if there are no edges, just to show negative result json0 =str() #"{ data: { id: '" + gene + "'} },\n" for node in nodes_d: - json0 += "{ data: { id: '" + node + "'} },\n" + json0 += "{ data: { id: '" + node + "', nodecolor: '" + nodecolor + "' } },\n" return(json0) def generate_edges(data): json0=str() + edgeCnts={} for line in data.split("\n"): if len(line.strip())!=0: (source, cat, target, pmid, sent) = line.split("\t") - edgeID=source+"_"+target - json0+="{ data: { id: \'" + edgeID + "\', source: \'" + source + "\', target: '" + target + "\' } },\n" + edgeID=source+"|"+target + if edgeID in edgeCnts: + edgeCnts[edgeID]+=1 + else: + edgeCnts[edgeID]=1 + for edgeID in edgeCnts: + (source,target)=edgeID.split("|") + json0+="{ data: { id: \'" + edgeID + "\', source: \'" + source + "\', target: '" + target + "\', sentCnt: '" + str(edgeCnts[edgeID]) + "' } },\n" return(json0) + + addiction_d = {"reward":"reward|reinforcement|conditioned place preference|CPP|self-administration|self-administered", - "aversion":"aversion|aversive|conditioned taste aversion|CTA|withdrawal", + "aversion":"aversion|aversive|CTA|withdrawal", "relapse":"relapse|reinstatement|craving|drug seeking", "sensitization":"sensitization", "addiction":"addiction|drug abuse", - "intoxication":"intoxication|binge", + "intoxication":"intoxication|binge" } addiction=undic(addiction_d) @@ -119,15 +128,9 @@ function_d={"plasticity":"LTP|LTD|plasticity|synaptic|epsp|epsc", } function=undic(function_d) -#out1=gene_anatomical(gene) -#out2=gene_functional(gene) -#report=out0+out1+out2 -#with codecs.open(gene+"_addiction_sentences.tab", "w", encoding='utf8') as writer: -# writer.write(report) -# writer.close() - -n0=generate_nodes(function_d) -n1=generate_nodes(addiction_d) -n2=generate_nodes(drug_d) -n3=generate_nodes(brain_d) +#https://htmlcolorcodes.com/ +n0=generate_nodes(function_d, "#D7BDE2") +n1=generate_nodes(addiction_d,"#A9CCE3") +n2=generate_nodes(drug_d, "#A3E4D7") +n3=generate_nodes(brain_d, "#F9E79F") default_nodes=n0+n1+n2+n3 |