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| author | Hao Chen | 2019-05-10 12:52:29 -0500 |
|---|---|---|
| committer | Hao Chen | 2019-05-10 12:52:29 -0500 |
| commit | 08503676ea318ade7a72fcd999a32bc6e5433e0c (patch) | |
| tree | 558aa9e2ee008540cc150fb1d08f5188fbcef9dc /cnt_gene_addiction_abstracts.py | |
| parent | 08c88ea579cbdb9dd89d4c6ca7906e5e729a2c64 (diff) | |
| download | genecup-08503676ea318ade7a72fcd999a32bc6e5433e0c.tar.gz | |
re run the quey if no result
Diffstat (limited to 'cnt_gene_addiction_abstracts.py')
| -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) |