Package obitools :: Package blast :: Class BlastMatch
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Class BlastMatch

source code


Blast high scoring pair between two sequences

Instance Methods [hide private]
 
getQueryLocation(self) source code
 
getSubjectLocation(self) source code
 
getSubjectSequence(self, database) source code
float
queryCov(self, query=None)
Compute coverage of match on query sequence.
source code
 
__getitem__(self, key) source code

Inherited from table.TableRow: __init__, __iter__, __len__, __repr__, __setitem__, __str__, append, castRow, extend, getColCount, getHIndex, getHeaders, getType, pop

Inherited from table.TableRow (private): _castRow

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Static Methods [hide private]

Inherited from table.TableRow (private): _castValue

Properties [hide private]

Inherited from table.TableRow: headers, types

Inherited from table.TableRow (private): _colcount, _hindex

Inherited from object: __class__

Method Details [hide private]

queryCov(self, query=None)

source code 

Compute coverage of match on query sequence.

Parameters:
  • query (obitools.BioSequence) - the query sequence. Default is None. In this case the query sequence associated to this blast result is used.
Returns: float
coverage fraction

__getitem__(self, key)
(Indexing operator)

source code 
Parameters:
  • key
Overrides: table.TableRow.__getitem__
(inherited documentation)