diff options
Diffstat (limited to 'ratspub.py')
| -rwxr-xr-x | ratspub.py | 27 |
1 files changed, 16 insertions, 11 deletions
@@ -3,6 +3,8 @@ from nltk.tokenize import sent_tokenize import os import re +global function_d, brain_d, drug_d, addiction_d + ## turn dictionary (synonyms) to regular expression def undic(dic): return "|".join(dic.values()) @@ -67,27 +69,28 @@ def gene_functional(gene): out+=gene+"\t"+"function\t"+bio0+"\t"+sent+"\n" return(out) -def generate_nodes(nodes_d, nodecolor): +def generate_nodes(nodes_d, nodetype): + nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7"} # include all search terms even if there are no edges, just to show negative result - json0 =str() #"{ data: { id: '" + gene + "'} },\n" + json0 =str() for node in nodes_d: - json0 += "{ data: { id: '" + node + "', nodecolor: '" + nodecolor + "' } },\n" + json0 += "{ data: { id: '" + node + "', nodecolor: '" + nodecolor[nodetype] + "', nodetype: '"+nodetype + "', url:'/shownode?nodetype=" + nodetype + "&node="+node+"' } },\n" return(json0) -def generate_edges(data): +def generate_edges(data, filename): 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 + edgeID=filename+"|"+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]) + "', url:'/sentences?edgeID=" + edgeID + "' } },\n" + (filename, source,target)=edgeID.split("|") + json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: '" + str(edgeCnts[edgeID]) + "', url:'/sentences?edgeID=" + edgeID + "' } },\n" return(json0) addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|ICSS|reinforcement|conditioned place preference|CPP|self administration|self administered|drug reinforced|operant|instrumental response", @@ -126,9 +129,11 @@ function_d={"neuroplasticity":"neuroplasticity|plasticity|long term potentiation } function=undic(function_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") +n0=generate_nodes(function_d, 'function') +n1=generate_nodes(addiction_d, 'addiction') +n2=generate_nodes(drug_d, 'drug') +n3=generate_nodes(brain_d, 'brain') default_nodes=n0+n1+n2+n3 |