ost.bindings.kclust Namespace Reference

Data Structures
class	cluster

Functions
	_SetupFiles (sequences)
	_CleanupFiles (tmp_dir_name)
	_ParseOutput (tmp_dir_name)
	_RunkClust (tmp_dir_name, clustering_thresh, create_alignments)
	kClust (sequences, clustering_thresh=30, create_alignments=False)

Function Documentation

_CleanupFiles()

_CleanupFiles (   tmp_dir_name )

protected

Definition at line 52 of file kclust.py.

_ParseOutput()

_ParseOutput (   tmp_dir_name )

protected

Definition at line 57 of file kclust.py.

_RunkClust()

_RunkClust (   tmp_dir_name,   clustering_thresh,   create_alignments  )

protected

Definition at line 94 of file kclust.py.

_SetupFiles()

_SetupFiles (   sequences )

protected

Definition at line 45 of file kclust.py.

kClust()

kClust	(		sequences,
			clustering_thresh = 30,
			create_alignments = False
	)

Uses kClust to generate clusters of amino acid sequences.

:param sequences: All sequences you want to cluster. 
:type sequences: :class:`ost.seq.SequenceList`

:param clustering_thres: Sequence identity threshold to build clusters. Note,
                         that clustering_thresh is more a rule of thumb, since
                         compositional bias in the sequence can also play a role.
                         The value gets transformed in a bitscore, that is used
                         as an input parameter of kClust 

:param create_alignments: Flag, wether the alignments of the clusters get calculated.
                          Requires clustalw in the path.

:returns: A list of cluster instances

:raises: :class:`~ost.settings.FileNotFound` if kClust could not be located.

Definition at line 127 of file kclust.py.