Multi-Query HAQESAC controller
Copyright © 2009 Richard J. Edwards - See source code for GNU License Notice
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
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.
### ~~~ INPUT 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  # 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.
MultiHAQ REST Output formatsRun with
which is formatted as follows:
###~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~### # OUTFMT: ... contents for OUTFMT section ...
Available REST OutputsThere is currently no specific help available on REST output for this program.
© 2015 RJ Edwards. Contact: email@example.com.