Package biana :: Package BianaObjects :: Module sequenceUtilities :: Class BlastallParserIterator
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Class BlastallParserIterator

source code


Instance Methods [hide private]
 
__init__(self, fd_blastall_output, parse_detailed_alignments=False)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
__iter__(self) source code
 
parse_alignment_line(self, alignment_line_list, aligned_query, aligned_sbjct) source code
 
next(self) source code

Inherited from object: __delattr__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __str__

Class Variables [hide private]
  query_re = re.compile(r'Query=\s*(.+)\s*')
  letters_re = re.compile(r'\(\s*([,\d]+)\s*letters\s*')
  sbjct_re = re.compile(r'>([\w\d_\.\|]+)')
  length_re = re.compile(r'Length = ([,\d]+)')
  score_re = re.compile(r'Score\s+=\s+([\.\d]+)\s+bits\s+\((\d+)...
  score_option2_re = re.compile(r'Score\s+=\s+([\.\d]+)\s+\(([\....
  identities_re = re.compile(r'Identities\s+=\s+\d+/(\d+)\s+\((\...
  positives_re = re.compile(r'Positives\s+=\s+\d+/\d+\s+\((\d+)%...
  gaps_re = re.compile(r'Gaps\s+=\s+\d+/\d+\s+\((\d+)%\)')
  intervals_query_re = re.compile(r'Query:\s+(\d+)\s+(\S+)\s+(\d...
  sbjct_intervals_re = re.compile(r'Sbjct:\s+(\d+)\s+(\S+)\s+(\d...
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, fd_blastall_output, parse_detailed_alignments=False)
(Constructor)

source code 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

Class Variable Details [hide private]

score_re

Value:
re.compile(r'Score\s+=\s+([\.\d]+)\s+bits\s+\((\d+)\),\s+Expect\s+=\s+\
([\d\.e-]+)')

score_option2_re

Value:
re.compile(r'Score\s+=\s+([\.\d]+)\s+\(([\.\d]+)\s+bits\),\s+Expect\s+\
=\s+([\d\.e-]+)')

identities_re

Value:
re.compile(r'Identities\s+=\s+\d+/(\d+)\s+\((\d+)%\)')

positives_re

Value:
re.compile(r'Positives\s+=\s+\d+/\d+\s+\((\d+)%\)')

intervals_query_re

Value:
re.compile(r'Query:\s+(\d+)\s+(\S+)\s+(\d+)$')

sbjct_intervals_re

Value:
re.compile(r'Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)$')