From 852126b92fdbe143f80ab52005d3d5da263178cb Mon Sep 17 00:00:00 2001 From: Jumitti Date: Thu, 10 Oct 2024 20:42:29 +0200 Subject: [PATCH] Minor improvements --- tfinder/__init__.py | 33 +++++++++++++++++---------------- 1 file changed, 17 insertions(+), 16 deletions(-) diff --git a/tfinder/__init__.py b/tfinder/__init__.py index e23b5106..7d5811a6 100644 --- a/tfinder/__init__.py +++ b/tfinder/__init__.py @@ -438,25 +438,26 @@ def get_variant_info(entrez_id, variant): # Get gene information def all_variant(entrez_id, from_id=False): - while True: - url2 = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={entrez_id}&retmode=json&rettype=xml" - response = requests.get(url2, headers=headers) + if not from_id: + while True: + url2 = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&id={entrez_id}&retmode=json&rettype=xml" + response = requests.get(url2, headers=headers) - if response.status_code == 200: - response_data = response.json() - try: - gene_info = response_data['result'][str(entrez_id)] - chraccver = gene_info['genomicinfo'][0]['chraccver'] - break + if response.status_code == 200: + response_data = response.json() + try: + gene_info = response_data['result'][str(entrez_id)] + chraccver = gene_info['genomicinfo'][0]['chraccver'] + break - except Exception as e: - all_variants = [("Error 200", None, None, None, None, None)] - return "Error 200", f"Transcript not found(s) for {entrez_id}." + except Exception as e: + all_variants = [("Error 200", None, None, None, None, None)] + return "Error 200", f"Transcript not found(s) for {entrez_id}." - elif response.status_code == 429: - time.sleep(random.uniform(0.25, 0.5)) - else: - time.sleep(random.uniform(0.25, 0.5)) + elif response.status_code == 429: + time.sleep(random.uniform(0.25, 0.5)) + else: + time.sleep(random.uniform(0.25, 0.5)) while True: url = f"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id={entrez_id}&retmode=xml"