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Biskit
Biskit :: Blast2Seq :: Blast2Seq :: Class Blast2Seq
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Class Blast2Seq

source code

Determine sequence identity between 2 protein sequences

Instance Methods [hide private]
  __init__(self, seq1, seq2, **kw)
  prepare(self)
create temporary fasta files for bl2seq
  cleanup(self)
remove temporary files
dict filterBlastHit(self)
Extract sequence identity and overlap length from one single bl2seq hit
  finish(self)
Overrides Executor method

Method Details [hide private]

__init__(self, seq1, seq2, **kw)
(Constructor)

source code 
Parameters:
  • seq1 (str) - sequence string
  • seq2 (str) - sequence string

prepare(self)

source code 

create temporary fasta files for bl2seq

cleanup(self)

source code 

remove temporary files

filterBlastHit(self)

source code 

Extract sequence identity and overlap length from one single bl2seq hit
Returns: dict
{'aln_id':1.0, 'aln_len':120}

finish(self)

source code 

Overrides Executor method

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