1 files changed, 0 insertions, 83 deletions
diff --git a/get_addiction_sentences.py b/get_addiction_sentences.py
deleted file mode 100644
index 30a8e50..0000000
--- a/get_addiction_sentences.py
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/bin/env python3 
-from nltk.tokenize import sent_tokenize
-import os
-import re
-import codecs
-import sys
-
-gene=sys.argv[1]
-
-addiction_terms="sensitization|intake|addiction|drug abuse|relapse|self-administered|self-administration|voluntary|reinstatement|binge|intoxication|withdrawal|chronic"
-
-drugs="alcohol|alcoholism|smoking|nicotine|tobacco|methamphetamine|amphetamine|cocaine|opioid|fentanyl|oxycodone|oxycontin|heroin|morphine|marijuana|cannabinoid|tetrahydrocannabinol|thc"
-
-brain_regions="cortex|accumbens|striatum|amygadala|hippocampus|tegmental|mesolimbic|infralimbic|prelimbic"
-
-brain_d ={"cortex":"cortex|pfc|vmpfc|il|pl|prelimbic|infralimbic",
-          "striatum":"striatum|STR",
-          "accumbens":"shell|core|NAcc|acbs|acbc",
-          "hippocampus":"hippocampus|hipp|hip|ca1|ca3|dentate|gyrus",
-          "amygadala":"amygadala|cea|bla|amy",
-          "ventral tegmental":"ventral tegmental|vta"
-          }
-
-function="LTP|LTD|plasticity|regulate|glutamate|GABA|cholinergic|serotoninergic|synaptic|methylation|transcription|phosphorylation"
-
-drugs_d = {"alcohol":"alcohol|alcoholism",
-        "nicotine":"smoking|nicotine|tobacco",
-        "amphetamine":"methamphetamine|amphetamine",
-        "cocaine":"cocaine",
-        "opioid":"opioid|fentanyl|oxycodone|oxycontin|heroin|morphine",
-        "cannabinoid":"marijuana|cannabinoid|Tetrahydrocannabinol|thc"
-        }
-
-def findWholeWord(w):
-    return re.compile(r'\b({0})\b'.format(w), flags=re.IGNORECASE).search
-
-def getSentences(query):
-    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").read()
-    out=str()
-    for row in abstracts.split("\n"):
-        tiab=row.split("\t")
-        pmid = tiab.pop(0)
-        tiab= " ".join(tiab)
-        sentences = sent_tokenize(tiab)
-        for sent in sentences:
-            if findWholeWord(gene)(sent):
-                sent=re.sub(r'\b(%s)\b' % gene, r'<b>\1</b>', sent, flags=re.I)
-                out+=pmid+"\t"+sent+"\n"
-    return(out)
-
-def gene_addiction(gene):
-    q="\"(" + addiction_terms.replace("|", " OR ")  + ") AND (" + drugs.replace("|", " OR ", ) + ") AND " + gene + "\""
-    sents=getSentences(q)
-    out=str()
-    for sent in sents.split("\n"):
-        for drug0 in drugs_d:
-            if findWholeWord(drugs_d[drug0])(sent) :
-                sent=re.sub(r'\b(%s)\b' % drugs_d[drug0], r'<b>\1</b>', sent, flags=re.I)
-                out+=gene+"\t"+drug0+"\t"+sent+"\n"
-    return(out)
-
-def gene_brainRegion(gene):
-    q="\"(" + brain_regions.replace("|", " OR ")  + ") AND " + gene + "\""
-    sents=getSentences(q)
-    out=str()
-    for sent in sents.split("\n"):
-        for brain0 in brain_d:
-            if findWholeWord(brain_d[brain0])(sent) :
-                sent=re.sub(r'\b(%s)\b' % brain_d[brain0], r'<b>\1</b>', sent, flags=re.I)
-                out+=gene+"\t"+brain0+"\t"+sent+"\n"
-    return(out)
-
-report=str()
-out=gene_addiction(gene)
-report+=out
-out=gene_brainRegion(gene)
-report+=out
-with codecs.open(gene+"_addiction_sentences.tab", "w", encoding='utf8') as writer:
-   writer.write(report)
-   writer.close()
-
-
-