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rje_ancseq V1.3

Ancestral Sequence Prediction Module

Module: rje_ancseq
Description: Ancestral Sequence Prediction Module
Version: 1.3
Last Edit: 24/07/13

Copyright © 2005 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_pam


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

Function

This module contains the objects and methods for ancestral sequence prediction. Currently, only GASP (Edwards & Shields 2004) is implemented. Other methods may be incorporated in the future.

GASP Commandline

fixpam=X\t: PAM distance fixed to X [0].
rarecut=X\t: Rare aa cut-off [0.05].
fixup=T/F\t: Fix AAs on way up (keep probabilities) [True].
fixdown=T/F\t: Fix AAs on initial pass down tree [False].
ordered=T/F\t: Order ancestral sequence output by node number [False].
pamtree=T/F\t: Calculate and output ancestral tree with PAM distances [True].
desconly=T/F\t: Limits ancestral AAs to those found in descendants [True].
xpass=X\t: How many extra passes to make down & up tree after initial GASP [1].

Classes

Gasp(log=None,cmd_list=[],tree=None,ancfile='gasp'):
- Handles main GASP algorithm.
>> log:Log = rje.Log object
>> cmd_list:List = List of commandline variables
>> tree:Tree = rje_tree.Tree Object
>> ancfile:str = output filename (basefile))
GaspNode(realnode,alphabet,log):
- Used by Gasp Class to handle specific node data during GASP.
>> realnode:Node Object (rje_tree.py)
>> alphabet:list of amino acids for use in GASP
>> log:Log Object

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - No Out Object in Objects
    # 1.0 - Better documentation for GASP V:1.2
    # 1.1 - Neatened up
    # 1.2 - Added 'RST Text' to gaspnode.rst list containing RST file-style data
    # 1.3 - Changed "biproblem" error handling in gaspProbs()

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.