Package Bio :: Package Compass :: Class _Consumer
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Class _Consumer


Method Summary
  __init__(self)
  hit_alignment(self, line)
  lengths(self, line)
  names(self, line)
Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln...
  positive_alignment(self, line)
  profilewidth(self, line)
  query_alignment(self, line)
  scores(self, line)
  threshold(self, line)

Class Variable Summary
SRE_Pattern _re_align = ^.{15}(\S+)
SRE_Pattern _re_lengths = length1=(\S+)\s+filtered_length1=(\S+)\s+l...
SRE_Pattern _re_names = Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+
SRE_Pattern _re_positive_alignment = ^.{15}(.+)
SRE_Pattern _re_profilewidth = Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(...
SRE_Pattern _re_scores = Smith-Waterman score = (\S+)\s+Evalue = (\S...
SRE_Pattern _re_start = (\d+)
SRE_Pattern _re_threshold = Threshold of effective gap content in co...

Method Details

names(self, line)

Ali1: 60456.blo.gz.aln  Ali2: allscop//14984.blo.gz.aln
      ------query-----        -------hit-------------

Class Variable Details

_re_align

Type:
SRE_Pattern
Value:
^.{15}(\S+)                                                            

_re_lengths

Type:
SRE_Pattern
Value:
length1=(\S+)\s+filtered_length1=(\S+)\s+length2=(\S+)\s+filtered_leng\
th2=(\S+)                                                              

_re_names

Type:
SRE_Pattern
Value:
Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+                                       

_re_positive_alignment

Type:
SRE_Pattern
Value:
^.{15}(.+)                                                             

_re_profilewidth

Type:
SRE_Pattern
Value:
Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(\S+)\s+Neff2=(\S+)                

_re_scores

Type:
SRE_Pattern
Value:
Smith-Waterman score = (\S+)\s+Evalue = (\S+)                          

_re_start

Type:
SRE_Pattern
Value:
(\d+)                                                                  

_re_threshold

Type:
SRE_Pattern
Value:
Threshold of effective gap content in columns: (\S+)                   

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