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 125 of file kclust.py.

 All Data Structures Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Defines

Generated on 20 Jun 2016 for OpenStructure by  doxygen 1.6.1