[Biopython-dev] [Bug 2929] New: NCBIXML PSI-Blast parser should gather all information from XML blastgpg output

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2929

           Summary: NCBIXML PSI-Blast parser should gather all information
                    from XML blastgpg output
           Product: Biopython
           Version: 1.52
          Platform: Macintosh
        OS/Version: Mac OS
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: ibdeno at gmail.com


With the problems encountered while parsing plain text output from blastpgp,
perhaps an answer would be to use the XML output of this program. The XML
output seems to have evolved in recent versions of blastpgp and now all the
info gets in a single proper XML file (not several concatenated files) and, in
principle, it would seem that all the information in the plain text format can
also be found in the XML one.

I will attach an XML output for a PSI-Blast search that converges after 3
passes.


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