max retmax as an argument in id mapping

NCBI-Hackathons · Mar 21, 2018 · 705a4e6 · 705a4e6
1 parent 054e70a
commit 705a4e6
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/dc/utils.py b/dc/utils.py
@@ -8,23 +8,23 @@
 Entrez.email = "hsiaoyi0504@gmail.com"
 
 
-def get_pubmed_ids_from_phenotypes(phenotypes):
+def get_pubmed_ids_from_phenotypes(phenotypes, retmax=200):
     pubmed_ids = []
     for phen in phenotypes:
         query = phen
-        handle = Entrez.esearch(db='pubmed', term=query, rettype='medline', retmode='text', retmax=200)
+        handle = Entrez.esearch(db='pubmed', term=query, rettype='medline', retmode='text', retmax=retmax)
         record = Entrez.read(handle)
         handle.close()
         idList = record['IdList']
         pubmed_ids.extend(idList)
     return list(set(pubmed_ids))
 
 
-def get_pubmed_ids_from_rsids(rsids):
+def get_pubmed_ids_from_rsids(rsids, retmax=200):
     pubmed_ids = []
     for id in rsids:
         query = 'rs' + id + 'AND pubmed_snp_cited[sb]'
-        handle = Entrez.esearch(db='pubmed', term=query, rettype="medline", retmode="text", retmax=200)
+        handle = Entrez.esearch(db='pubmed', term=query, rettype="medline", retmode="text", retmax=retmax)
         record = Entrez.read(handle)
         handle.close()
         idList = record['IdList']