Program: SeqForker Description: Generic Sequence Analysis Forking Script Version: 1.0 Last Edit: 23/09/05

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

Imported modules: rje rje_seq

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

Function

This module is designed to take a large input sequence dataset, split it into chunks, fork out the chunks to some process and then stick all the results back together at the end. It is designed to be flexible and work for any analyses where each sequence is looked at independently and filenames can be given to the program performing the analysis.

Commandline

seqin=FILE : Input sequence file [None]
split=X : Number of sequences per split file [0]
startfrom=X : Will pick up program at this sequence, where X is the name or accession number [None]
* Remember to set append=T if picking up a crashed run *
append=T/F : Will append to results files rather than overwrite [False]
forkprog=PATH : Common program system call for all forked splits of sequence file (e.g. program) [None]
forkcmd="blah blah" : Common system commands for all forked splits of sequence file (e.g. program options) [None]
outcmd=X : Command line option for giving output file name. Will be altered to match forked splits (*.*) [None]
seqincmd=X : Command given to program for input file name [seqin=]
* SeqForker will stitch together "forkprog seqincmd=FILE forkcmd outcmd" *

General Commandline

v=X : Sets verbosity (-1 for silent) [0]
i=X : Sets interactivity (-1 for full auto) [0]
log=FILE : Redirect log to FILE [Default = calling_program.log]
newlog=T/F : Create new log file. [Default = False: append log file]

Forking Commandline

noforks=T/F : Whether to avoid forks [False]
forks=X : Number of parallel sequences to process at once [0]
killforks=X : Number of seconds of no activity before killing all remaining forks. [3600]