diff options
| -rwxr-xr-x | cnt_gene_addiction_abstracts.py | 7 |
1 files changed, 4 insertions, 3 deletions
diff --git a/cnt_gene_addiction_abstracts.py b/cnt_gene_addiction_abstracts.py index c216862..f55586f 100755 --- a/cnt_gene_addiction_abstracts.py +++ b/cnt_gene_addiction_abstracts.py @@ -8,6 +8,10 @@ from ratspub import * def gene_addiction_cnt(gene): q="\"(" + addiction.replace("|", "[tiab] OR ") + ") AND (" + drug.replace("|", "[tiab] OR ", ) + ") AND (" + gene + ")\"" count=os.popen('esearch -db pubmed -query ' + q + ' | xtract -pattern ENTREZ_DIRECT -element Count ').read() + if (len(count)==0): + print("pause") + time.sleep(15) + gene_addiction_cnt(gene) return (count) out=open("gene_addiction_cnt_result_part1.tab", "w+") @@ -25,9 +29,6 @@ with open ("./ncbi_gene_symb_syno_txid9606_part1.txt", "r") as f: gene_q=gene.replace("|", " [tiab] OR ") gene_q+="[tiab]" count=gene_addiction_cnt(gene_q) - if (len(count)==0): - print("pause") - time.sleep(10) print(gene+"\t"+count) out.write(gene+"\t"+count) |