Package Biskit :: Package Mod :: Module NCBIStandalone :: Class _Scanner

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Class _Scanner

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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

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

_scan_header(self, uhandle, consumer)

_scan_rounds(self, uhandle, consumer)

_scan_descriptions(self, uhandle, consumer)

_scan_alignments(self, uhandle, consumer)

_scan_pairwise_alignments(self, uhandle, consumer)

_scan_one_pairwise_alignment(self, uhandle, consumer)

_scan_alignment_header(self, uhandle, consumer)

_scan_hsp(self, uhandle, consumer)

_scan_hsp_header(self, uhandle, consumer)

_scan_hsp_alignment(self, uhandle, consumer)

_scan_masterslave_alignment(self, uhandle, consumer)

_scan_database_report(self, uhandle, consumer)

_scan_parameters(self, uhandle, consumer)

Method Details

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feed(S, handle, consumer)

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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.

_scan_header(self, uhandle, consumer)

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_scan_rounds(self, uhandle, consumer)

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_scan_descriptions(self, uhandle, consumer)

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_scan_alignments(self, uhandle, consumer)

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_scan_pairwise_alignments(self, uhandle, consumer)

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_scan_one_pairwise_alignment(self, uhandle, consumer)

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_scan_alignment_header(self, uhandle, consumer)

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_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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_scan_database_report(self, uhandle, consumer)

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_scan_parameters(self, uhandle, consumer)

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