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Diffstat (limited to 'more_functions.py')
| -rwxr-xr-x | more_functions.py | 165 |
1 files changed, 165 insertions, 0 deletions
diff --git a/more_functions.py b/more_functions.py new file mode 100755 index 0000000..234330b --- /dev/null +++ b/more_functions.py @@ -0,0 +1,165 @@ +#!/bin/env python3 +from nltk.tokenize import sent_tokenize +import os +import re + +from nltk.util import pr +from addiction_keywords import * +from gene_synonyms import * +import ast +from flask import session + +global pubmed_path + +def undic(dic): + all_s='' + for s in dic: + all_s += "|".join(str(e) for e in s) + all_s +="|" + all_s=all_s[:-1] + return all_s + +def findWholeWord(w): + return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search + +def getabstracts(gene,query): + if query[-1] =='s': + query2 = query+"*" + else: + query2 = query+"s*" + query3 = query2.replace("s|", "s* OR ") + query4 = query3.replace("|", "s* OR ") + query="\"(" + query4 + ") AND " + gene + "\"" + abstracts = os.popen("esearch -db pubmed -query " + query \ + + " | efetch -format uid |fetch-pubmed -path "+ pubmed_path \ + + " | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read() + return(abstracts) + +sentences_ls=[] +def getSentences(gene, sentences_ls): + out=str() + # Keep the sentence only if it contains the gene + for sent in sentences_ls: + if gene.lower() in sent.lower(): + pmid = sent.split(' ')[0] + sent = sent.split(' ',1)[1] + sent=re.sub(r'\b(%s)\b' % gene, r'<strong>\1</strong>', sent, flags=re.I) + out+=pmid+"\t"+sent+"\n" + return(out) + +def gene_category(gene, cat_d, cat, abstracts,addiction_flag,dictn): + # e.g. BDNF, addiction_d, undic(addiction_d) "addiction" + sents=getSentences(gene, abstracts) + out=str() + if (addiction_flag==1): + for sent in sents.split("\n"): + for key in cat_d: + if findWholeWord(cat_d[key])(sent) : + sent=sent.replace("<b>","").replace("</b>","") # remove other highlights + sent=re.sub(r'\b(%s)\b' % cat_d[key], r'<b>\1</b>', sent, flags=re.I) # highlight keyword + out+=gene+"\t"+ cat + "\t"+key+"\t"+sent+"\n" + else: + for sent in sents.split("\n"): + for key_1 in dictn[cat_d].keys(): + for key_2 in dictn[cat_d][key_1]: + if findWholeWord(key_2)(sent) : + sent=sent.replace("<b>","").replace("</b>","") # remove other highlights + sent=re.sub(r'\b(%s)\b' % key_2, r'<b>\1</b>', sent, flags=re.I) # highlight keyword + out+=gene+"\t"+ cat + "\t"+key_1+"\t"+sent+"\n" + return(out) + +def generate_nodes(nodes_d, nodetype,nodecolor): + # Include all search terms even if there are no edges, just to show negative result + json0 =str() + for node in nodes_d: + json0 += "{ data: { id: '" + node + "', nodecolor: '" + nodecolor + "', nodetype: '"+nodetype + "', url:'/shownode?nodetype=" + nodetype + "&node="+node+"' } },\n" + return(json0) + +def generate_nodes_json(nodes_d, nodetype,nodecolor): + # 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 + "\", \"url\":\"/shownode?nodetype=" + nodetype + "&node="+node+"\" },\n" + return(nodes_json0) + +def generate_edges(data, filename): + pmid_list=[] + 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+target not in pmid_list): + edgeCnts[edgeID]+=1 + pmid_list.append(pmid+target) + elif (edgeID not in edgeCnts) and (pmid+target not in pmid_list): + edgeCnts[edgeID]=1 + pmid_list.append(pmid+target) + + 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 generate_edges_json(data, filename): + pmid_list=[] + 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+target not in pmid_list): + edgeCnts[edgeID]+=1 + pmid_list.append(pmid+target) + elif (edgeID not in edgeCnts) and (pmid+target not in pmid_list): + edgeCnts[edgeID]=1 + pmid_list.append(pmid+target) + + 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,sents, path_user): + if sets=='topGene': + dataFile="topGene_addiction_sentences.tab" + nodes= "{ data: { id: '" + query + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n" + elif sets=='GWAS': + dataFile="gwas_addiction.tab" + nodes=str() + pmid_list=[] + catCnt={} + sn_file = '' + + for sn in sents: + (symb, cat0, cat1, pmid, sent)=sn.split("\t") + if (symb.upper() == query.upper()) : + if (cat1 in catCnt.keys()) and (pmid+cat1 not in pmid_list): + pmid_list.append(pmid+cat1) + catCnt[cat1]+=1 + elif (cat1 not in catCnt.keys()): + catCnt[cat1]=1 + pmid_list.append(pmid+cat1) + sn_file += sn + '\n' + + nodes= "{ data: { id: '" + query + "', nodecolor: '" + "#2471A3" + "', fontweight:700, url:'/progress?query="+query+"' } },\n" + edges=str() + gwas_json=str() + nodecolor={} + nodecolor["GWAS"]="hsl(0, 0%, 70%)" + + for key in catCnt.keys(): + 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" + edgeID=path_user+'gwas_results.tab'+"|"+query+"|"+key + edges+="{ data: { id: '" + edgeID+ "', source: '" + query + "', target: '" + key + "', sentCnt: " + str(catCnt[key]) + ", url:'/sentences?edgeID=" + edgeID + "' } },\n" + gwas_json+="{ \"id\": \"" + edgeID + "\", \"source\": \"" + query + "\", \"target\": \"" + key + "\", \"sentCnt\": \"" + str(catCnt[key]) + "\", \"url\":\"/sentences?edgeID=" + edgeID + "\" },\n" + return(nodes+edges,gwas_json,sn_file) + +pubmed_path=os.environ["EDIRECT_PUBMED_MASTER"] + |