From bc84bbc6bec82f4cddbba4e84e855965bea267a2 Mon Sep 17 00:00:00 2001
From: chen42
Date: Wed, 25 Mar 2026 16:48:59 -0500
Subject: update requirements
---
ratspub.py | 167 -------------------------------------------------------------
1 file changed, 167 deletions(-)
delete mode 100755 ratspub.py
(limited to 'ratspub.py')
diff --git a/ratspub.py b/ratspub.py
deleted file mode 100755
index 5621b5e..0000000
--- a/ratspub.py
+++ /dev/null
@@ -1,167 +0,0 @@
-#!/bin/env python3
-from nltk.tokenize import sent_tokenize
-import os
-import re
-from ratspub_keywords import *
-from gene_synonyms import *
-
-global function_d, brain_d, drug_d, addiction_d, brain_query_term, pubmed_path, genes
-
-## turn dictionary (synonyms) to regular expression
-def undic(dic):
- return "|".join(dic.values())
-
-def findWholeWord(w):
- return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search
-
-def getSentences(query, 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()
- out=str()
- for row in abstracts.split("\n"):
- tiab=row.split("\t")
- pmid = tiab.pop(0)
- tiab= " ".join(tiab)
- sentences = sent_tokenize(tiab)
- ## keep the sentence only if it contains the gene
- for sent in sentences:
- if findWholeWord(gene)(sent):
- sent=re.sub(r'\b(%s)\b' % gene, r'\1', sent, flags=re.I)
- out+=pmid+"\t"+sent+"\n"
- return(out)
-
-def gene_category(gene, cat_d, query, cat):
- #e.g. BDNF, addiction_d, undic(addiction_d) "addiction"
- q="\"(" + query.replace("|", " OR ") + ") AND " + gene + "\""
- sents=getSentences(q, gene)
- out=str()
- for sent in sents.split("\n"):
- for key in cat_d:
- if findWholeWord(cat_d[key])(sent) :
- sent=sent.replace("","").replace("","") # remove other highlights
- sent=re.sub(r'\b(%s)\b' % cat_d[key], r'\1', sent, flags=re.I) # highlight keyword
- out+=gene+"\t"+ cat + "\t"+key+"\t"+sent+"\n"
- return(out)
-
-def generate_nodes(nodes_d, nodetype):
- # 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: '"+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_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):
- 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()
- 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()) 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)
-
- 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"]
- 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"]
- nodes += "{ data: { id: '" + key + "', nodecolor: '" + nc + "', url:'/shownode?node="+key+"' } },\n"
- else:
- nc=nodecolor["addiction"]
- 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"
- 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)
-
-gene_s=undic(genes)
-
-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')
-n6=''
-
-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=''
-
-pubmed_path=os.environ["EDIRECT_PUBMED_MASTER"]
-
--
cgit 1.4.1