From 15dde5133ac6d72846aa0db631e6660d50cb904e Mon Sep 17 00:00:00 2001
From: Hao Chen
Date: Sun, 19 Apr 2020 12:02:28 -0500
Subject: mv some files to utility

---
 topGene_step2_cnt_sentences.py | 65 ------------------------------------------
 1 file changed, 65 deletions(-)
 delete mode 100755 topGene_step2_cnt_sentences.py

(limited to 'topGene_step2_cnt_sentences.py')

diff --git a/topGene_step2_cnt_sentences.py b/topGene_step2_cnt_sentences.py
deleted file mode 100755
index b05aa7a..0000000
--- a/topGene_step2_cnt_sentences.py
+++ /dev/null
@@ -1,65 +0,0 @@
-#!/bin/env python3 
-import os, sys
-import re
-import time
-from nltk.tokenize import sent_tokenize
-from ratspub_keywords import *
-
-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, genes):
-    abstracts = os.popen("esearch -db pubmed -query " +  query + " | efetch -format uid |fetch-pubmed -path /run/media/hao/PubMed/Archive/ | xtract -pattern PubmedArticle -element MedlineCitation/PMID,ArticleTitle,AbstractText|sed \"s/-/ /g\"").read()
-    gene_syno=genes.split("|")
-    symb=gene_syno[0]
-    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:
-            for gene in gene_syno:
-                if findWholeWord(gene)(sent):
-                    sent=re.sub(r'\b(%s)\b' % gene, r'<strong>\1</strong>', sent, flags=re.I)
-                    for drug0 in drug_d:
-                        if findWholeWord(drug_d[drug0])(sent) :
-                            sent=sent.replace("<b>","").replace("</b>","")
-                            sent=re.sub(r'\b(%s)\b' % drug_d[drug0], r'<b>\1</b>', sent, flags=re.I)
-                            out+=symb+"\t"+"drug\t" + drug0+"\t"+pmid+"\t"+sent+"\n"
-                    for add0 in addiction_d:
-                        if findWholeWord(addiction_d[add0])(sent) :
-                            sent=sent.replace("<b>","").replace("</b>","")
-                            sent=re.sub(r'\b(%s)\b' % addiction_d[add0], r'<b>\1</b>', sent, flags=re.I)
-                            out+=symb+"\t"+"addiction\t"+add0+"\t"+pmid+"\t"+sent+"\n"
-    return(out)
-
-addiction=undic(addiction_d)
-drug=undic(drug_d)
-
-
-out=open("topGene_addiction_sentences.tab", "w+")
-cnt=0
-
-if len(sys.argv) != 2:
-    print ("Please provide a sorted gene count file at the command line")
-    sys.exit()
-
-sorted_file=sys.argv[1] #  ncbi_gene_symb_syno_name_txid9606_absCnt_sorted_absCnt_sorted_absCnt_sorted_absCnt_sorted.txt
-with open (sorted_file, "r") as f:
-    for line in f:
-        (genes, abstractCount)=line.strip().split("\t")
-        genes=genes.replace("-","\ ")
-        if int(abstractCount)>20:
-            symb=genes.split("|")[0]
-            print(symb+"-->"+genes)
-            q="\'(\"" + addiction.replace("|", "\"[tiab] OR \"")  + "\") AND (\"" + drug.replace("|", "\"[tiab] OR \"", ) + "\") AND (\"" + genes.replace("|", "\"[tiab] OR \"", ) + "\")\'"
-            sentences=getSentences(q,genes)
-            out.write(sentences)
-out.close()
-
-os.system("cut -f 1,4 topGene_addiction_sentences.tab  |uniq |cut -f 1 |sort |uniq -c |sort -rn > topGeneAbstractCount.tab")
-- 
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