I used to be able to use BioPython to blast the wgs database at NCBI using the following handle:
NCBIWWW.qblast(program="blastn", database= "wgs" sequence=fasta_string, entrez_query= organism + '[ORGN]')
This does not appear to work anymore, and returns an xml with no results. For searches in wgs the taxon must be specified, and I have previously used the entrez_query parameter to do this. In the web interface this is not available and there is a "limit by" field which has to be filled in instead. Does anybody know how to specify the "limit by" parameter in BioPython or to specify other parameters that may be required for the wgs blast? It is a bit frustrating when scripts stop working because of changes in the ncbi interface.
Thanks in advance