Sorry for the odd name.
I use eSearch and eSummary to go from
Access Number → gID → TaxID
Suppose a “join” is a list of 20 access numbers (I do 20 at a time, because the maximum that the NCBI allows).
I do:
handle = Entrez.esearch(db="nucleotide", rettype="xml", term=accessions)
record = Entrez.read(handle)
gids = ",".join(record[u'IdList'])
This gives me 20 matching GIDs from these 20 registration numbers.
The following are:
handle = Entrez.esummary(db="nucleotide", id=gids)
record = Entrez.read(handle)
Which gives me this error, because one of the GIDs in the gids has been removed from the NCBI:
File ".../biopython-1.52/build/lib.macosx-10.6-universal-2.6/Bio/Entrez/Parser.py", line 191, in endElement value = IntegerElement(value)
ValueError: invalid literal for int() with base 10: ''
I could try: except: except that it will skip the other 19 GIDs which are ok.
My question is:
20 Entrez.read , , 20? , ( 300 000 , NCBI 3 , 1 ).