Module: rje_slimcalc Description: SLiM Attribute Calculation Module Version: 0.10.0 Last Edit: 20/03/18

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

Imported modules: rje rje_zen rje_aaprop rje_disorder rje_seq rje_sequence rje_slim rje_scoring gopher ned_eigenvalues

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

Function

This module is based on the old rje_motifstats module. It is primarily for calculating empirical attributes of SLiMs and their occurrences, such as Conservation, Hydropathy and Disorder.

Commandline

#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### Motif Occurrence Attribute Options ###
slimcalc=LIST : List of additional attributes to calculate for occurrences - Cons,SA,Hyd,Fold,IUP,Chg,Comp []
winsize=X : Used to define flanking regions for calculations. If negative, will use flanks *only* [0]
relconwin=X : Window size for relative conservation scoring [30]
iupath=PATH : The full path to the IUPred exectuable [c:/bioware/iupred/iupred.exe]
iucut=X : Cut-off for IUPred results (0.0 will report mean IUPred score) [0.0]
iumethod=X : IUPred method to use (long/short) [short]
percentile=X : Percentile steps to return in addition to mean [0]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### Alignment Settings ###
usealn=T/F : Whether to search for and use alignments where present. [False]
alndir=PATH : Path to pre-made alignment files [./]
alnext=X : File extension of alignment files, AccNum.X (checked before Gopher used) [orthaln.fas]
gopherdir=PATH : Path from which to look for GOPHER alignments (if not found in alndir) and/or run GOPHER [./]
usegopher=T/F : Use GOPHER to generate orthologue alignments missing from alndir - see gopher.py options [False]
fullforce=T/F : Whether to force regeneration of alignments using GOPHER [False]
orthdb=FILE : File to use as source of orthologues for GOPHER []
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### Conservation Parameters ###
conspec=LIST : List of species codes for conservation analysis. Can be name of file containing list. [None]
conscore=X : Type of conservation score used: [rlc]
- abs = absolute conservation of motif using RegExp over matched region
- pos = positional conservation: each position treated independently
- prob = conservation based on probability from background distribution
- prop = conservation of amino acid properties
- rlc = relative local conservation
- all = all methods for comparison purposes
consamb=T/F : Whether to calculate conservation allowing for degeneracy of motif (True) or of fixed variant (False) [True]
consinfo=T/F : Weight positions by information content (does nothing for conscore=abs) [True]
consweight=X : Weight given to global percentage identity for conservation, given more weight to closer sequences [0]
- 0 gives equal weighting to all. Negative values will upweight distant sequences.
minhom=X : Minimum number of homologues for making conservation score [1]
homfilter=T/F : Whether to filter homologues using seqfilter options [False]
alngap=T/F : Whether to count proteins in alignments that have 100% gaps over motif (True) or (False) ignore
as putative sequence fragments [False] (NB. All X regions are ignored as sequence errors.)
posmatrix=FILE : Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) [None]
aaprop=FILE : Amino Acid property matrix file. [aaprop.txt]
masking=T/F : Whether to use seq.info['MaskSeq'] for Prob cons, if present (else 'Sequence') [True]
vnematrix=FILE : BLOSUM matrix file to use for VNE relative conservation []
relgappen=T/F : Whether to invoke the "Gap Penalty" during relative conservation calculations [True]
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
### SLiM/Occ Filtering Options ###
slimfilter=LIST : List of stats to filter (remove matching) SLiMs on, consisting of X*Y []
- X is an output stat (the column header),
- * is an operator in the list >, >=, !=, =, >= ,<
- Y is a value that X must have, assessed using *.
This filtering is crude and may behave strangely if X is not a numerical stat!
!!! Remember to enclose in "quotes" for <> filtering !!!
occfilter=LIST : Same as slimfilter but for individual occurrences []
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#

History Module Version History

    # 0.0 - Initial Compilation based on rje_motifstats methods.
    # 0.1 - Added new probability-based method, inspired by (but different to) Dinkel & Sticht (2007)
    # 0.2 - Mended OccPos finding for wildcards. Added new relative conservation score.
    # 0.3 - Added von Neumann entropy code.
    # 0.4 - Added Webserver pickling of RLC lists.
    # 0.5 - Altered to use GOPHER V3 and handle nested alignment directories.
    # 0.6 - Minor tweak to avoid unwanted GOPHER directory generation.
    # 0.7 - Added RLC to "All" conscore running.
    # 0.8 - Made RLC the default.
    # 0.9 - Improvements to use of GOPHER.
    # 0.9.1 - Modified combining of motif stats to handle expectString format for individual values.
    # 0.9.2 - Changed default conscore in docstring to RLC.
    # 0.9.3 - Changed fudge error to warning.
    # 0.10.0 - Added extra disorder methods to slimcalc.