Biskit :: Hmmer :: HmmerSearch :: Class HmmerSearch

Class HmmerSearch

Search hmm database (using the hmmpfam program) with a sequence in fasta format. If the profile names have been provided - skip the search and only write the temporary sequence files.

Instance Methods

[hide private]

__init__(self, target, hmmdb, noSearch=None, **kw)

True/False __verify_fasta(self, target)
Verify that a given file or string is in Fasta format.

prepare(self)
If the target id a PDBModel its sequence will be written to disc as a fasta file.

dict, [list] parse_result(self)
Parse the output from hmmpfam.

finish(self)
Overrides Executor method

Method Details

[hide private]

init(self, target, hmmdb, noSearch=None, **kw)
(Constructor)

source code

Parameters:

target (PDBModel or fasta file) - sequence
hmmdb (str) - Pfam hmm database
noSearch (1 OR None) - don't perform a seach

__verify_fasta(self, target)

source code

Verify that a given file or string is in Fasta format. The definition used for a fasta file here is that:

first line starts with '>'
the following sequence lines are not longer that 80 characters
the characters has to belong to the standard amino acid codes

Parameters:

target (str OR [str]) - name of fasta file OR file contents as list of strings

Returns: True/False: conforms to the fsata format

prepare(self)

source code

If the target id a PDBModel its sequence will be written to disc as a fasta file. If it is a fasta file the path to the file will be passed on.

parse_result(self)

source code

Parse the output from hmmpfam.

Returns: dict, [list]: dictionary witn profile names as keys and a list of lists containing information about the range where the profile matches the sequence

finish(self)

source code

Overrides Executor method

Class HmmerSearch

__init__(self, target, hmmdb, noSearch=None, **kw) (Constructor)

__verify_fasta(self, target)

prepare(self)

parse_result(self)

finish(self)

init(self, target, hmmdb, noSearch=None, **kw)
(Constructor)