diff options
| -rwxr-xr-x | more_functions.py | 43 | ||||
| -rw-r--r-- | requirements.md | 3 | ||||
| -rwxr-xr-x | server.py | 15 |
3 files changed, 33 insertions, 28 deletions
diff --git a/more_functions.py b/more_functions.py index cb070d9..7c21c2a 100755 --- a/more_functions.py +++ b/more_functions.py @@ -23,21 +23,10 @@ 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 ") - - #query4=query - #query="\"(" + query4 + ") AND ((" + gene + "[tiab]) or (" + gene + "[meSH]))\"" - query="\"(" + query4 + ") AND (" + gene + " [tiab])\"" - #query = "neurons* AND (penk [tiab])" + query="\"(" + query + ") AND (" + gene + " [tiab])\"" 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() - #print(abstracts) return(abstracts) sentences_ls=[] @@ -57,6 +46,7 @@ def getSentences(gene, sentences_ls): def gene_category(gene, cat_d, cat, abstracts,addiction_flag,dictn): # e.g. BDNF, addiction_d, undic(addiction_d) "addiction" sents=getSentences(gene, abstracts) + #print(sents) #print(abstracts) out=str() if (addiction_flag==1): @@ -66,10 +56,16 @@ def gene_category(gene, cat_d, cat, abstracts,addiction_flag,dictn): key_ad = key+"*" else: key_ad = key+"s*" - if findWholeWord(key_ad)(sent) : - sent=sent.replace("<b>","").replace("</b>","") # remove other highlights - sent=re.sub(r'\b(%s)\b' % key_ad, r'<b>\1</b>', sent, flags=re.I) # highlight keyword - out+=gene+"\t"+ cat + "\t"+key+"\t"+sent+"\n" + key_ad = key_ad.replace("s|", "s*|") + key_ad = key_ad.replace("|", "s*|") + key_ad = key_ad.replace("s*s*", "s*") + key_ad_ls = key_ad.split('|') + for key_ad in key_ad_ls: + re_find = re.compile(r'\b{}\b'.format(key_ad), re.IGNORECASE) + if re_find.findall(sent): + sent=sent.replace("<b>","").replace("</b>","") # remove other highlights + sent=re.sub(r'\b(%s)\b' % key_ad, r'<b>\1</b>', sent, flags=re.I) # highlight keyword + out+=gene+"\t"+ cat + "\t"+key+"\t"+sent+"\n" else: for key_1 in dictn[cat_d].keys(): for key_2 in dictn[cat_d][key_1]: @@ -77,11 +73,17 @@ def gene_category(gene, cat_d, cat, abstracts,addiction_flag,dictn): key_2 = key_2+"*" else: key_2 = key_2+"s*" + key_2 = key_2.replace("s|", "s*|") + key_2 = key_2.replace("|", "s*|") + key_2 = key_2.replace("s*s*", "s*") + key_2_ls = key_2.split('|') for sent in sents.split("\n"): - 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" + for key_2 in key_2_ls: + re_find = re.compile(r'\b{}\b'.format(key_2), re.IGNORECASE) + if re_find.findall(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): @@ -134,7 +136,6 @@ def generate_edges_json(data, filename): 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" diff --git a/requirements.md b/requirements.md index 7b90aec..8824016 100644 --- a/requirements.md +++ b/requirements.md @@ -47,5 +47,4 @@ * tensorflow-estimator==2.4.0 -* python==3.8.5 - +* python==3.8.5
\ No newline at end of file @@ -146,7 +146,6 @@ def login(): else: flash("Invalid username or password!", "inval") return render_template('signup.html') - print(onto_list) return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) @@ -570,7 +569,11 @@ def ontoarchive(): if ('email' in session): if os.path.exists(datadir+"/user/"+str(session['hashed_email'])+"/ontology") == False: flash("Ontology history doesn't exist!") - return render_template('index.html',onto_len_dir=session['onto_len_dir'], onto_list=session['onto_list']) + onto_len_dir = 0 + onto_list = '' + onto_cont=open("addiction.onto","r").read() + dict_onto=ast.literal_eval(onto_cont) + return render_template('index.html',onto_len_dir=onto_len_dir, onto_list=onto_list, ontol = 'addiction', dict_onto = dict_onto) else: session['user_folder'] = datadir+"/user/"+str(session['hashed_email']) else: @@ -762,7 +765,7 @@ def search(): if(len(genes)==1): percent_ratio=2 timeextension=session['timeextension'] - percent=round(100/percent_ratio,1)-1 # 7 categories + 1 at the beginning + percent=100/percent_ratio-0.00000001 # 7 categories + 1 at the beginning if ('email' in session): sessionpath = session['path_user'] + timeextension @@ -852,6 +855,7 @@ def search(): yield "data:"+str(progress)+"\n\n" for gene in genes: abstracts_raw = getabstracts(gene,all_d) + #print(abstracts_raw) sentences_ls=[] for row in abstracts_raw.split("\n"): @@ -891,10 +895,11 @@ def search(): dict_onto=ast.literal_eval(onto_cont) #ky_d=undic(list(dict_onto[ky].values())) sent=gene_category(gene,ky,str(ky), sentences_ls, addiction_flag,dict_onto) - else: #ky_d=undic(list(dict_onto[ky].values())) + #print(sentences_ls) sent=gene_category(gene,ky,str(ky), sentences_ls, addiction_flag,dict_onto) + #print(sent) yield "data:"+str(progress)+"\n\n" geneEdges += generate_edges(sent, tf_name) @@ -918,7 +923,7 @@ def search(): +str(row['MAPPED_TRAIT'])+"</b><br>" gwas_sent.append(gene+"\t"+"GWAS"+"\t"+nd+"_GWAS\t"+str(row['PUBMEDID'])+"\t"+gwas_text) cys, gwas_json, sn_file = searchArchived('GWAS', gene , 'json',gwas_sent, path_user) - with open(path_user+"gwas_results.tab", "w") as gwas_edges: + with open(path_user+"gwas_results.tab", "a") as gwas_edges: gwas_edges.write(sn_file) geneEdges += cys json_edges += gwas_json |