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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Dec 10 07:27:07 EST 2004


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
 Attachment #187 is|0                           |1
           obsolete|                            |

------- Additional Comments From biopython-bugzilla at maubp.freeserve.co.uk  2004-12-10 07:26 -------
Created an attachment (id=188)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=188&action=view)
Edited version of NCBIStandalone.py based on CVS revision 1.57

As per attachment 187 with a further refinement to cope with an error

If blastall 2.2.10 is given an empty input file (0 bytes) it produces no ouput.

However, rpsblast 2.2.10 will produce a single line of output, the version

This means that while parsing the header we should check for this possible end
of file, and issue a helpful error message.

This revision has been tested on both Linux, Windows 2000 and Windows XP.

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