[Biopython-dev] [Bug 2588] New: tutorial blast section uses undefined variables

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2588

           Summary: tutorial blast section uses undefined variables
           Product: Biopython
           Version: 1.48
          Platform: Other
        OS/Version: All
            Status: NEW
          Severity: trivial
          Priority: P2
         Component: Documentation
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: bsouthey at gmail.com


Tutorial Section 6.6.2  'Parsing a file full of BLAST runs' has line:
>>> blast_iterator = NCBIStandalone.Iterator(blast_handle, blast_parser)

but 'blast_handle' is undefined. This line should probably be:
>>> blast_iterator = NCBIStandalone.Iterator(result_handle, blast_parser)

where result_handle is define in Section 6.6.1  'Parsing plain-text BLAST
output':
>>> result_handle = open("my_file_of_blast_output.txt")

Also:
>>> for b_record in b_iterator :

probably should be:
>>> for b_record in blast_iterator :


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