diff options
Diffstat (limited to 'ncbi/dbsnp/ncbiutils.py')
| -rw-r--r-- | ncbi/dbsnp/ncbiutils.py | 26 |
1 files changed, 22 insertions, 4 deletions
diff --git a/ncbi/dbsnp/ncbiutils.py b/ncbi/dbsnp/ncbiutils.py index b3c199a..9bc1c94 100644 --- a/ncbi/dbsnp/ncbiutils.py +++ b/ncbi/dbsnp/ncbiutils.py @@ -2,10 +2,11 @@ import requests -BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" - -# Example https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=snp&term=snp_pubmed_cited[sb]&retmax=200000&retstart=1000&retmode=json -def db_query(**kwargs): +""" +Used to make an esearch and get the results back in json +""" +def esearch(**kwargs): + BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?" args = [] for key, value in kwargs.items(): args.append(key+"="+str(value)) @@ -15,4 +16,21 @@ def db_query(**kwargs): results = resp.json() return(results) else: + print("You've encountered an error and we can't return your results") + +""" +Used for an efetch, which is primarily to query specific IDs in dbsnp or pubmed +Doesn't return json, but must return XML, apparently. +""" +def efetch(**kwargs): + BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?" + args = [] + for key, value in kwargs.items(): + args.append(key+"="+str(value)) + qstring = "&".join(args) + resp = requests.get(BASE_URL + qstring) + if resp.status_code == 200: + results = resp.text + return(results) + else: print("You've encountered an error and we can't return your results")
\ No newline at end of file |