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Data Structures | Functions
ost.bindings.kclust Namespace Reference

Data Structures

class  cluster
 

Functions

def kClust
 

Function Documentation

def ost.bindings.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.