Package Bio :: Package Blast :: Module NCBIStandalone :: Class _Scanner

Class _Scanner

object --+
         |
        _Scanner

Scan BLAST output from blastall or blastpgp.

Tested with blastall and blastpgp v2.0.10, v2.0.11

Methods:
feed     Feed data into the scanner.

Instance Methods

[hide private]

feed(S, handle, consumer)
Feed in a BLAST report for scanning.

source code

_scan_header(self, uhandle, consumer)

source code

_scan_rounds(self, uhandle, consumer)

source code

_scan_descriptions(self, uhandle, consumer)

source code

_scan_alignments(self, uhandle, consumer)

source code

_scan_pairwise_alignments(self, uhandle, consumer)

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_scan_one_pairwise_alignment(self, uhandle, consumer)

source code

_scan_alignment_header(self, uhandle, consumer)

source code

_scan_hsp(self, uhandle, consumer)

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_scan_hsp_header(self, uhandle, consumer)

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_scan_hsp_alignment(self, uhandle, consumer)

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_scan_masterslave_alignment(self, uhandle, consumer)

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_eof(self, uhandle)

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_scan_database_report(self, uhandle, consumer)

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_scan_parameters(self, uhandle, consumer)

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Inherited from object: __delattr__, __getattribute__, __hash__, __init__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

feed(S, handle, consumer)

source code

Feed in a BLAST report for scanning.  handle is a file-like
object that contains the BLAST report.  consumer is a Consumer
object that will receive events as the report is scanned.