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rje_taxmap V0.5.1

Mapping taxonomic groups onto sequences based on Newick trees.

Module: rje_taxmap
Description: Mapping taxonomic groups onto sequences based on Newick trees.
Version: 0.5.1
Last Edit: 08/01/19

Copyright © 2016 Richard J. Edwards - See source code for GNU License Notice


Imported modules: rje rje_obj rje_db rje_tree rje_taxonomy


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

Function

The function of this module will be added here.

Outputs for subsets of Newick files can be generated by giving a set of *.class files (or set classify=FILELIST).

Commandline

Input Options

nwklist=FILES : List of Newick format files. (*.nwk names must match accnum.) Wildcards allowed. [*.nwk]
protdesc=FILE : Delimited file of protein, description [None]
classify=FILELIST : List of files containing protein IDs (first column) for additional taxsum outputs [*.class]
basefile=X : Base for output files. Will reuse unless force=T ['taxmap']
taxbase=X : Base of previous run to load results from, if not basefile []

Taxon Assignment Options

minboot=X : Minimum bootstrap value for an "in-clade" with query protein [0.5]
noneboot=X : Bootstrap support to give "None" ratings [1.0]
minscore=X : Filter out species codes with score < minscore [1.0]
minsum=X : Convert taxa with score < minsum to "Other" for *.taxsum.tdt output [10.0]
minclass=X : Convert taxa with score < minclass to "Other" for *.CLASS.tdt output [1.0]
bootweight=T/F : Whether to weight taxon scores for each protein by clade bootstrap support for filtering [True]
bootfilter=X : Filter bootstrap support < X to "Uncertain" [0.0]
monophyly=T/F : Enforce strict monophyly and change any multiple assignments to "Uncertain" [False]
taxfilter=LIST : List of taxonomic assignments to filter from rank/summary (e.g. "Uncertain") []


History Module Version History

    # 0.0.0 - Initial Compilation.
    # 0.1.0 - Initial Working Version.
    # 0.2.0 - Added bootstraps and minscore.
    # 0.2.1 - Fixed missing species names in *.taxa.tdt output.
    # 0.3.0 - Added monophyly=T/F   : Enforce strict monophyly and change any multiple assignments to "Uncertain" [False]
    # 0.4.0 - Added TaxFilter, minsum=X and classify=FILELIST files containing protein IDs (first column) for additional taxsum outputs [*.class]
    # 0.5.0 - Fixed the filtering of Unmapped taxa when other (mapped) taxa are present.
    # 0.5.1 - Minor bug fix for classes with blank lines.

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