Module: rje_haq Description: Homologue Alignment Quality module Version: 1.3 Last Edit: 21/02/07

Copyright © 2007 Richard J. Edwards - See source code for GNU License Notice

---

Imported modules: rje

---

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

HAQ of HAQESAC: SAQ and PAQ methods from haqesac.

NB. The classes in this module are designed to take sequence objects and perform analyses, not create sequence objects themselves if none are given. The module haqesac.py will do this.

Commandline

noquery=T/F : No Query for SAQ, Random Query for PAQ
saqc=X : Min no. seqs to share residue in SAQ. [2]
saqb=X : SAQ Block length. [10]
saqm=X : No. residues to match in SAQ Block. [7]
saqks=X : Relative Weighting of keeping Sequences in SAQ. [3]
saqkl=X : Relative Weighting of keeping Length in SAQ. [1]
mansaq=T/F : Manual over-ride of sequence rejection decisions in SAQ [False]
paqb=X : PAQ Block length. [7]
paqm=X : No. residues to match in PAQ Block. [3]
paqks=X : Relative Weighting of keeping Sequences in PAQ. [3]
paqkl=X : Relative Weighting of keeping Length in PAQ. [1]
manpaq=T/F : Manual over-ride of sequence rejection decisions in PAQ [False]
anchors=T/F : Whether to use conserved 'anchors' to extend well-aligned regions in PAQ [True]