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Biskit :: Hmmer :: HmmerAlign :: Class HmmerAlign
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Class HmmerAlign

source code

Align fasta formated sequence to hmm profile (using hmmalign).

Instance Methods [hide private]
  __init__(self, hmmFile, fastaFile, fastaID, **kw)
str, str parse_result(self)
Align fasta formated sequence to hmm profile.
  fail(self)
Called if external program failed, override!
  finish(self)
Overrides Executor method

Method Details [hide private]

__init__(self, hmmFile, fastaFile, fastaID, **kw)
(Constructor)

source code 
Parameters:
  • hmmFile (str) - path to hmm file (profile)
  • fastaFile (str) - path to fasta search sequence
  • fastaID (str) - fasta id of search sequence

parse_result(self)

source code 

Align fasta formated sequence to hmm profile.
Returns: str, str
alignment and matching hmm positions with gaps

fail(self)

source code 

Called if external program failed, override!

finish(self)

source code 

Overrides Executor method

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