Package Bio :: Package Blast :: Module NCBIStandalone :: Class _Scanner
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Class _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.
Method Summary
  _scan_alignment_header(self, uhandle, consumer)
  _scan_alignments(self, uhandle, consumer)
  _scan_database_report(self, uhandle, consumer)
  _scan_descriptions(self, uhandle, consumer)
  _scan_header(self, uhandle, consumer)
  _scan_hsp(self, uhandle, consumer)
  _scan_hsp_alignment(self, uhandle, consumer)
  _scan_hsp_header(self, uhandle, consumer)
  _scan_masterslave_alignment(self, uhandle, consumer)
  _scan_one_pairwise_alignment(self, uhandle, consumer)
  _scan_pairwise_alignments(self, uhandle, consumer)
  _scan_parameters(self, uhandle, consumer)
  _scan_rounds(self, uhandle, consumer)
  feed(self, handle, consumer)
S.feed(handle, consumer)

Method Details

feed(self, handle, consumer)

S.feed(handle, consumer)

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.

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