Package Bio :: Package Compass :: Class _Scanner
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Class _Scanner

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Reads compass output and generate events (OBSOLETE)

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

_scan_alignment(self, handle, consumer)

source code 

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


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