diff options
Diffstat (limited to 'ratspub.py')
| -rwxr-xr-x | ratspub.py | 74 |
1 files changed, 61 insertions, 13 deletions
@@ -48,43 +48,79 @@ def generate_nodes(nodes_d, nodetype): json0 += "{ data: { id: '" + node + "', nodecolor: '" + nodecolor[nodetype] + "', nodetype: '"+nodetype + "', url:'/shownode?nodetype=" + nodetype + "&node="+node+"' } },\n" return(json0) +def generate_nodes_json(nodes_d, nodetype): + # include all search terms even if there are no edges, just to show negative result + nodes_json0 =str() + for node in nodes_d: + nodes_json0 += "{ \"id\": \"" + node + "\", \"nodecolor\": \"" + nodecolor[nodetype] + "\", \"nodetype\": \"" + nodetype + "\", \"url\":\"/shownode?nodetype=" + nodetype + "&node="+node+"\" },\n" + return(nodes_json0) + def generate_edges(data, filename): + pmid_temp=0 json0=str() edgeCnts={} for line in data.split("\n"): if len(line.strip())!=0: (source, cat, target, pmid, sent) = line.split("\t") edgeID=filename+"|"+source+"|"+target - if edgeID in edgeCnts: + if (edgeID in edgeCnts) and (pmid != pmid_temp): edgeCnts[edgeID]+=1 - else: + pmid_temp = pmid + elif (edgeID not in edgeCnts): edgeCnts[edgeID]=1 + pmid_temp = pmid for edgeID in edgeCnts: (filename, source,target)=edgeID.split("|") json0+="{ data: { id: '" + edgeID + "', source: '" + source + "', target: '" + target + "', sentCnt: " + str(edgeCnts[edgeID]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" return(json0) -def searchArchived(sets, query): +def generate_edges_json(data, filename): + pmid_temp=0 + edges_json0=str() + edgeCnts={} + for line in data.split("\n"): + if len(line.strip())!=0: + (source, cat, target, pmid, sent) = line.split("\t") + edgeID=filename+"|"+source+"|"+target + if (edgeID in edgeCnts) and (pmid != pmid_temp): + edgeCnts[edgeID]+=1 + pmid_temp = pmid + elif (edgeID not in edgeCnts): + edgeCnts[edgeID]=1 + pmid_temp = pmid + for edgeID in edgeCnts: + (filename, source,target)=edgeID.split("|") + edges_json0+="{ \"id\": \"" + edgeID + "\", \"source\": \"" + source + "\", \"target\": \"" + target + "\", \"sentCnt\": \"" + str(edgeCnts[edgeID]) + "\", \"url\":\"/sentences?edgeID=" + edgeID + "\" },\n" + return(edges_json0) + +def searchArchived(sets, query, filetype): if sets=='topGene': dataFile="topGene_addiction_sentences.tab" nodes= "{ data: { id: '" + query + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n" - elif sets=='gwas': + + elif sets=='GWAS': dataFile="gwas_addiction.tab" nodes=str() with open(dataFile, "r") as sents: + pmid_list=[] + cat1_list=[] catCnt={} for sent in sents: (symb, cat0, cat1, pmid, sent)=sent.split("\t") if (symb.upper() == query.upper()) : - if cat1 in catCnt.keys(): + if (cat1 in catCnt.keys()) and (pmid+cat1 not in pmid_list): + pmid_list.append(pmid+cat1) catCnt[cat1]+=1 - else: + elif (cat1 not in catCnt.keys()): catCnt[cat1]=1 + pmid_list.append(pmid+cat1) + nodes= "{ data: { id: '" + query + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n" edges=str() + gwas_json=str() for key in catCnt.keys(): - if sets=='gwas': - nc=nodecolor["gwas"] + if sets=='GWAS': + nc=nodecolor["GWAS"] nodes += "{ data: { id: '" + key + "', nodecolor: '" + nc + "', url:'https://www.ebi.ac.uk/gwas/search?query="+key.replace("_GWAS","")+"' } },\n" elif key in drug_d.keys(): nc=nodecolor["drug"] @@ -94,23 +130,35 @@ def searchArchived(sets, query): nodes += "{ data: { id: '" + key + "', nodecolor: '" + nc + "', url:'/shownode?node="+key+"' } },\n" edgeID=dataFile+"|"+query+"|"+key edges+="{ data: { id: '" + edgeID+ "', source: '" + query + "', target: '" + key + "', sentCnt: " + str(catCnt[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" - return(nodes+edges) - + gwas_json+="{ \"id\": \"" + edgeID + "\", \"source\": \"" + query + "\", \"target\": \"" + key + "\", \"sentCnt\": \"" + str(catCnt[key]) + "\", \"url\":\"/sentences?edgeID=" + edgeID + "\" },\n" + if(filetype == 'cys'): + return(nodes+edges) + else: + return(gwas_json) # brain region has too many short acronyms to just use the undic function, so search PubMed using the following brain_query_term="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic|habenula" function=undic(function_d) addiction=undic(addiction_d) drug=undic(drug_d) -nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'gwas':"#AEB6BF", 'stress':"#EDBB99", 'psychiatric':"#F5B7B1"} +nodecolor={'function':"#A9CCE3", 'addiction': "#D7BDE2", 'drug': "#F9E79F", 'brain':"#A3E4D7", 'GWAS':"#AEB6BF", 'stress':"#EDBB99", 'psychiatric':"#F5B7B1"} #https://htmlcolorcodes.com/ third column down + n0=generate_nodes(function_d, 'function') n1=generate_nodes(addiction_d, 'addiction') n2=generate_nodes(drug_d, 'drug') n3=generate_nodes(brain_d, 'brain') n4=generate_nodes(stress_d, 'stress') n5=generate_nodes(psychiatric_d, 'psychiatric') -default_nodes=n0+n1+n2+n3+n4+n5 +n6=generate_nodes(psychiatric_d, 'GWAS') + +nj0=generate_nodes_json(function_d, 'function') +nj1=generate_nodes_json(addiction_d, 'addiction') +nj2=generate_nodes_json(drug_d, 'drug') +nj3=generate_nodes_json(brain_d, 'brain') +nj4=generate_nodes_json(stress_d, 'stress') +nj5=generate_nodes_json(psychiatric_d, 'psychiatric') +nj6=generate_nodes_json(psychiatric_d, 'GWAS') host= os.popen('hostname').read().strip() if host=="x1": @@ -118,4 +166,4 @@ if host=="x1": elif host=="hchen3": pubmed_path="/media/hao/2d554499-6c5b-462d-85f3-5c49b25f4ac8/PubMed/Archive" elif host=="penguin2": - pubmed_path="/export2/PubMed/Archive" + pubmed_path="/export2/PubMed/Archive"
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