Module: rje_hmm Description: HMMer Control Module Version: 1.3 Last Edit: 25/11/08

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

Imported modules: rje rje_blast rje_zen

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

Function

This module is designed to perform basic HMM functions using the HMMer program. Currently, there are three functions that may be performed, separately or consecutively:

• 1. Use hmmbuild to construct HMMs from input sequence files
• 2. Search a sequence database with HMMs files
• 3. Convert HMMer output into a delimited text file of results.

Commandline

## Build Options ##
makehmm=LIST : Sequence file(s). Can include wildcards [None]
hmmcalibrate=T/F : Whether to calibrate HMM files once made [True]
## Search Options ##
hmm=LIST : HMM file(s). Can include wildcards. [*.hmm]
searchdb=FILE : Fasta file to search with HMMs [None]
hmmoptions=LIST : List or file of additional HMMer search options (joined by whitespace) []
hmmpfam=T/F : Performs standard HMMer PFam search (--cut_ga) (or processes if present) [False]
hmmout=FILE : Pipe results of HMM searches into FILE [None]
hmmres=LIST : List of HMM search results files to convert (wildcards allowed) []
hmmtab=FILE : Delimited table of results ('None' to skip) [searchdb.tdt]
cleanres=T/F : Option to reduce size of HMM results file by removing no-hit sequences [True]
## System Parameters ##
hmmerpath=PATH : Path for hmmer files [/home/richard/Bioware/hmmer-2.3.2/src/]
force=T/F : Whether to force regeneration of new HMMer results if already existing [False]
gzip=T/F : Whether to gzip (and gunzip) HMMer results files (not Windows) [True]

Classes

HMMRun Object = Full HMM run
HMMSearch Object = Information for a single Query search within a BLASTRun
HMMHit Object = Detailed Information for a single Query-Hit pair within BLASTRun
rje_blast.PWAln Object = Detailed Information for each aligned section of a Query-Hit Pair

History Module Version History

    # 0.0 - Initial Working Compilation.
    # 1.0 - Working version with multiple HMM capacity
    # 1.1 - Added hmmpfam option
    # 1.2 - Cleaned up and debugged for rje_ensembl.ensDat()
    # 1.3 - Minor updates.