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

source code

Instance Methods [hide private]
 
__init__(self) source code
 
names(self, line)
Ali1: 60456.blo.gz.aln Ali2: allscop//14984.blo.gz.aln...
source code
 
threshold(self, line) source code
 
lengths(self, line) source code
 
profilewidth(self, line) source code
 
scores(self, line) source code
 
query_alignment(self, line) source code
 
positive_alignment(self, line) source code
 
hit_alignment(self, line) source code
Class Variables [hide private]
  _re_names = re.compile(r'Ali1:\s+(\S+)\s+Ali2:\s+(\S+)\s+')
  _re_threshold = re.compile(r'Threshold of effective gap conten...
  _re_lengths = re.compile(r'length1=(\S+)\s+filtered_length1=(\...
  _re_profilewidth = re.compile(r'Nseqs1=(\S+)\s+Neff1=(\S+)\s+N...
  _re_scores = re.compile(r'Smith-Waterman score = (\S+)\s+Evalu...
  _re_start = re.compile(r'(\d+)')
  _re_align = re.compile(r'^.{15}(\S+)')
  _re_positive_alignment = re.compile(r'^.{15}(.+)')
Method Details [hide private]

names(self, line)

source code 

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


Class Variable Details [hide private]

_re_threshold

Value:
re.compile(r'Threshold of effective gap content in columns: (\S+)')

_re_lengths

Value:
re.compile(r'length1=(\S+)\s+filtered_length1=(\S+)\s+length2=(\S+)\s+\
filtered_length2=(\S+)')

_re_profilewidth

Value:
re.compile(r'Nseqs1=(\S+)\s+Neff1=(\S+)\s+Nseqs2=(\S+)\s+Neff2=(\S+)')

_re_scores

Value:
re.compile(r'Smith-Waterman score = (\S+)\s+Evalue = (\S+)')