update requirements

1 files changed, 0 insertions, 167 deletions

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'<strong>\1</strong>', 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("<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"
-    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"]
-