Bio.Compass.

Package Bio :: Package Compass :: Class _Scanner

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Class _Scanner

Reads compass output and generate events

Method Summary
	`_scan_alignment(self, handle, consumer)` QUERY 2 LSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPN...
	`_scan_lengths(self, handle, consumer)` length1=388 filtered_length1=386 length2=145 filtered_length2=137
	`_scan_names(self, handle, consumer)` Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln
	`_scan_profilewidth(self, handle, consumer)` Nseqs1=399 Neff1=12.972 Nseqs2=1 Neff2=6.099
	`_scan_record(self, handle, consumer)`
	`_scan_scores(self, handle, consumer)` Smith-Waterman score = 37 Evalue = 5.75e+02
	`_scan_threshold(self, handle, consumer)` Threshold of effective gap content in columns: 0.5
	`feed(self, handle, consumer)` Feed in COMPASS ouput

Method Details

_scan_alignment(self, handle, consumer)

QUERY   2      LSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPN
               ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
QUERY   2      LSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPN


QUERY          IGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFV
               ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
QUERY          IGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFV

_scan_lengths(self, handle, consumer)

length1=388 filtered_length1=386 length2=145 filtered_length2=137

_scan_names(self, handle, consumer)

Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln

_scan_profilewidth(self, handle, consumer)

Nseqs1=399 Neff1=12.972 Nseqs2=1 Neff2=6.099

_scan_scores(self, handle, consumer)

Smith-Waterman score = 37 Evalue = 5.75e+02

_scan_threshold(self, handle, consumer)

Threshold of effective gap content in columns: 0.5

feed(self, handle, consumer)

Feed in COMPASS ouput

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