diff options
Diffstat (limited to 'more_functions.py')
| -rwxr-xr-x | more_functions.py | 30 |
1 files changed, 23 insertions, 7 deletions
diff --git a/more_functions.py b/more_functions.py index 234330b..cb070d9 100755 --- a/more_functions.py +++ b/more_functions.py @@ -29,18 +29,25 @@ def getabstracts(gene,query): query2 = query+"s*" query3 = query2.replace("s|", "s* OR ") query4 = query3.replace("|", "s* OR ") - query="\"(" + query4 + ") AND " + gene + "\"" + + #query4=query + #query="\"(" + query4 + ") AND ((" + gene + "[tiab]) or (" + gene + "[meSH]))\"" + query="\"(" + query4 + ") AND (" + gene + " [tiab])\"" + #query = "neurons* AND (penk [tiab])" 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() + #print(abstracts) return(abstracts) sentences_ls=[] def getSentences(gene, sentences_ls): out=str() # Keep the sentence only if it contains the gene + #print(sentences_ls) for sent in sentences_ls: - if gene.lower() in sent.lower(): + #if gene.lower() in sent.lower(): + if re.search(r'\b'+gene.lower()+r'\b',sent.lower()): pmid = sent.split(' ')[0] sent = sent.split(' ',1)[1] sent=re.sub(r'\b(%s)\b' % gene, r'<strong>\1</strong>', sent, flags=re.I) @@ -50,18 +57,27 @@ def getSentences(gene, sentences_ls): def gene_category(gene, cat_d, cat, abstracts,addiction_flag,dictn): # e.g. BDNF, addiction_d, undic(addiction_d) "addiction" sents=getSentences(gene, abstracts) + #print(abstracts) out=str() if (addiction_flag==1): for sent in sents.split("\n"): for key in cat_d: - if findWholeWord(cat_d[key])(sent) : + if key =='s': + key_ad = key+"*" + else: + key_ad = key+"s*" + if findWholeWord(key_ad)(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 + sent=re.sub(r'\b(%s)\b' % key_ad, r'<b>\1</b>', sent, flags=re.I) # highlight keyword out+=gene+"\t"+ cat + "\t"+key+"\t"+sent+"\n" else: - for sent in sents.split("\n"): - for key_1 in dictn[cat_d].keys(): - for key_2 in dictn[cat_d][key_1]: + for key_1 in dictn[cat_d].keys(): + for key_2 in dictn[cat_d][key_1]: + if key_2[-1] =='s': + key_2 = key_2+"*" + else: + key_2 = key_2+"s*" + for sent in sents.split("\n"): if findWholeWord(key_2)(sent) : sent=sent.replace("<b>","").replace("</b>","") # remove other highlights sent=re.sub(r'\b(%s)\b' % key_2, r'<b>\1</b>', sent, flags=re.I) # highlight keyword |