Program: MultiHAQ Description: Multi-Query HAQESAC controller Version: 1.5.0 Last Edit: 23/09/20 Citation: Jones, Edwards et al. (2011), Marine Biotechnology 13(3): 496-504.

Copyright © 2009 Richard J. Edwards - See source code for GNU License Notice

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Imported modules: haqesac rje rje_seq rje_seqlist rje_zen slimfarmer

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

Function

This module is a wrapper for multiple HAQESAC runs where different query proteins are to be BLASTed against the same search database(s) and run through HAQESAC with the same settings. The default expectation is that some queries will be returned by the HAQESAC runs of other queries and may therefore be skipped as a result, although this can be switched off using screenqry=F. For large runs, the first phase of MulitHAQ will take a long time to run. In these cases, it may be desirable to set the second, interactive, phase running before it has finished. This is achieved using the "chaser" option, which will set the second phase in motion, "chasing" the progress of the first. To avoid jumbled log output, this should be given a different log file using log=FILE.

Note: that all options will be output into a haqesac.ini file in the haqdir path, for both HAQESAC runs within the framework of MultiHAQ itself and also for later runs using the batch file produced. Any generic HAQESAC options should therefore be placed into a multihaq.ini file, not a haqesac.ini file and multiple runs with different settings using the same haqdir should be avoided.

Note: Because HAQESAC makes use of RJE_SEQ filtering options, they will NOT be applied to the MultiHAQ query input file prior to analysis. To filter this input, run it through rje_seq.py separately in advance of running multihaq.

Commandline

### ~~~ INPUT OPTIONS ~~~ ###
seqin=FILE : Input query sequences [None]
blast2fas=LIST : List of databases to BLAST queries against prior to HAQESAC []
addqueries=T/F : Whether to add query database to blast2fas list [True]
keepblast=T/F : Whether to keep BLAST results files [True]
blastcut=X : Restrict HAQESAC and MultiHAQ BLAST searches to top X BLAST hits [0]
multicut=X : Restrict MultiHAQ BLASTs to the top X hits from each database (over-rides blastcut) [0]
### ~~~ MULTIHAQ OPTIONS ~~~ ###
haqesac=T/F : Run HAQESAC (True) or limit to batch file output (False) [True]
multihaq=T/F : Whether to run HAQESAC in two-phase multihaq mode [True]
screenqry=T/F : Whether to look for queries in previous runs and give option to skip [True]
autoskip=T/F : Whether to automatically skip queries found in previous runs [False]
chaser=T/F : Option for running second phase of multihaq as second run whilst first run in progress [False]
force=T/F : Whether to force re-running of stages (True) or pick-up pre-existing runs (False) [False]
### ~~~ OUTPUT OPTIONS ~~~~ ###
haqdir=PATH : Directory in which to output HAQESAC files and perform run [seqin_HAQESAC]
haqblastdir=PATH: Directory in which MultiHAQ BLAST2FAS BLAST runs will be performed [./HAQBLAST/]

See also haqesac.py commands and rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added chaser and autoskip options.
    # 1.0 - Fully working version. Fixed minor basefile bug. Added blastcut filter.
    # 1.1 - Improved pickup of aborted run.
    # 1.2 - Changed defaults to autoskip=F.
    # 1.2.1 - Updated documentation to include the HAQESAC reference.
    # 1.2.2 - Switched default to keepblast=T. Added forking blasta=X command to BLAST.
    # 1.3.0 - MultiCut : Restrict BLAST to the top X hits from each database [100]
    # 1.4.0 - Added SLiMFarmer batch forking if autoskip=F and i=-1.
    # 1.4.1 - Added haqblastdir=PATH: Directory in which MultiHAQ BLAST2FAS BLAST runs will be performed [./HAQBLAST/]
    # 1.4.2 - Fixed issue with SLiMFarmer for i<0 runs.
    # 1.4.3 - Updated warnings if BLAST2FAS files not found.
    # 1.5.0 - Updated BLAST2FAS code to use rje_seqlist for speed up.

MultiHAQ REST Output formats

Run with &rest=docs for program documentation and options. A plain text version is accessed with &rest=help.
&rest=OUTFMT can be used to retrieve individual parts of the output, matching the tabs in the default
(&rest=format) output. Individual OUTFMT elements can also be parsed from the full (&rest=full) server output,
which is formatted as follows:

###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~###
# OUTFMT:
... contents for OUTFMT section ...

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Available REST Outputs

There is currently no specific help available on REST output for this program.