[Biopython-dev] [Bug 1715] Bio.Blast.NCBIStandalone does not support standalone NCBI RPS-Blast (rpsblast) output

Wed Dec 15 08:24:53 EST 2004

http://bugzilla.open-bio.org/show_bug.cgi?id=1715

------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2004-12-15 08:24 -------
Created an attachment (id=189)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=189&action=view)
RPS-BLAST 2.2.10 multi query output file for testing iterator support

This is another test file, again using RPS-BLAST 2.2.10 results on the Pfam
database, but with MULTIPLE INPUT QUERIES.

As can be seen from this sample output, unlike blastall, rpsblast does not
repeat the version string at the start of the second and subsequent queries.

As a result the NCBIStandalone.Iterator currently fails to spot multiple
queries.  The "Query= " line must be used instead.

The input queries were these three genes from Vibrio cholerae, extracted from
NC_002506.gbk, available here:

ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Vibrio_cholerae/NC_002506.gbk

The first entry, gi|15640033, is a small hypothetical protein (44 residues). 
This gives no hit results.

The second query, gi|15600773, is a larger hypothetical protein (658 residues),
giving ten poor hits.

The third query, also a hypothetical protein (204 letters) gives four poor
hits.