From c997194555fec42b1e879f5d702710d1941b6345 Mon Sep 17 00:00:00 2001
From: Hao Chen
Date: Mon, 13 May 2019 06:06:13 -0500
Subject: agaist top 150 addiction genes
---
ratspub.py | 8 +-
server.py | 50 +-
templates/cytoscape.html | 1 +
top_150_addiction_genes_uniq.pmid | 1443666 ++++++++++++++++++++++++++++++++++
top_150_genes_symb_alias.txt | 150 +
5 files changed, 1443870 insertions(+), 5 deletions(-)
create mode 100644 top_150_addiction_genes_uniq.pmid
create mode 100644 top_150_genes_symb_alias.txt
diff --git a/ratspub.py b/ratspub.py
index 7916198..355679c 100755
--- a/ratspub.py
+++ b/ratspub.py
@@ -102,17 +102,17 @@ addiction_d = {"reward":"reward|hedonic|incentive|intracranial self stimulation|
}
addiction=undic(addiction_d)
-drug_d = {"alcohol":"alcohol|alcoholism|alcoholic",
- "nicotine":"smoking|nicotine|tobacco",
+drug_d = {"alcohol":"alcohol|alcoholism|alcoholic|alcoholics",
+ "nicotine":"smoking|nicotine|tobacco|smoker|smokers",
"cocaine":"cocaine",
"opioid":"opioid|opioids|fentanyl|oxycodone|oxycontin|heroin|morphine|methadone|buprenorphine|vicodin|hydrocodone|hycodan|kadian|percoset|hydromorphone|naloxone|codeine|suboxone|tramadol|kratom",
"amphetamine":"methamphetamine|amphetamine|METH|AMPH",
- "cannabinoid":"endocannabinoid|cannabinoids|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides"
+ "cannabinoid":"endocannabinoid|cannabinoids|cannabis|endocannabinoids|marijuana|cannabidiol|cannabinoid|tetrahydrocannabinol|thc|thc 9|Oleoylethanolamide|palmitoylethanolamide|acylethanolamides"
}
drug=undic(drug_d)
brain_d ={"cortex":"cortex|prefrontal|pfc|mPFC|vmpfc|corticostriatal|cortico limbic|corticolimbic|prl|prelimbic|infralimbic|orbitofrontal|cingulate|cerebral|insular|insula",
- "striatum":"striatum|STR|striatal|caudate|putamen|basal ganglia|globus pallidus",
+ "striatum":"striatum|STR|striatal|caudate|putamen|basal ganglia|globus pallidus|GPI",
"accumbens":"accumbens|accumbal|shell|core|Nacc|NacSh|acbs|acbc",
"hippocampus":"hippocampus|hippocampal|hipp|hip|ca1|ca3|dentate gyrus|subiculum|vhipp|dhpc|vhpc",
"amygdala":"amygdala|cea|bla|amy",
diff --git a/server.py b/server.py
index 3c124d3..286f071 100755
--- a/server.py
+++ b/server.py
@@ -5,6 +5,7 @@ import random
import string
from ratspub import *
import time
+import os
app=Flask(__name__)
app.config['SECRET_KEY'] = '#DtfrL98G5t1dC*4'
@@ -46,7 +47,7 @@ def search():
nodes=default_nodes
progress=0
for gene in genes:
- nodes+="{ data: { id: '" + gene + "', nodecolor:'#FADBD8', fontweight:700, url:'https://www.ncbi.nlm.nih.gov/gene/?term="+gene+"'} },\n"
+ nodes+="{ data: { id: '" + gene + "', nodecolor:'#E74C3C', fontweight:700, url:'/gene_gene?gene="+gene+"'} },\n"
progress+=percent
yield "data:"+str(progress)+"\n\n"
sent0=gene_addiction(gene)
@@ -97,5 +98,52 @@ def shownode():
out=""+node.upper()+"
"+ allnodes[node].replace("|", "")
return render_template('sentences.html', sentences=out+"")
+@app.route("/gene_gene")
+def gene_gene():
+ query=request.args.get("gene")
+ tmp_ggPMID=session['path']+"_ggPMID"
+ os.system("esearch -db pubmed -query \"" + query + "\" | efetch -format uid |sort >" + tmp_ggPMID)
+ abstracts=os.popen("comm -1 -2 top_150_addiction_genes_uniq.pmid " + tmp_ggPMID + " |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
+ os.system("rm "+tmp_ggPMID)
+ topGenes=dict()
+ out=str()
+ hitGenes=dict()
+ with open("./top_150_genes_symb_alias.txt", "r") as top_f:
+ for line in top_f:
+ (symb, alias)=line.strip().split("\t")
+ topGenes[symb]=alias
+ 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(query)(sent):
+ sent=re.sub(r'\b(%s)\b' % query, r'\1', sent, flags=re.I)
+ for symb in topGenes:
+ if findWholeWord(topGenes[symb])(sent) :
+ sent=sent.replace("","").replace("","")
+ sent=re.sub(r'\b(%s)\b' % topGenes[symb], r'\1