Module: rje_hmm Description: HMMer Control Module Version: 2.0 Last Edit: 23/01/13

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

Imported modules: rje rje_db rje_obj rje_zen rje_blast_V1

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.

Version 2.x onwards are redeveloped to work with HMMER3.0. Please used rje_hmm_V1.py for legacy runs.

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
rje_db.Database Object = Stores detailed hit information as with the rje_blast V2.x module.

History Module Version History

    # 2.0 - Initial HMMER3.0 version based on Version 1.2 and RJE_BLAST 2.0.