NAME

createSubProject.pl

SYNOPSIS


  createSubProject.pl -is <454Scaffolds.txt> 
                      -ip <454Contigs.ace.1.pairs>    
                      -od <existing output dir or path> 
                      -of <full path for creation of sub project fof>
                      -sf <name of scaff info file to be created within each subproject>
                      -rl <ReadLinkage min ex 2> 
                      -ms <min Scaffold len ex 50000> 
                      -ic <ignore Circ gap 1=true 0=false>

  Note:all given options are required

DESCRIPTION

This script takes as input newbler generated 454Scaffolds.txt file and newblerAce2ReadPair.pl generated read pairs file. The output dir or path for output dir creation is specified.

Suproject directories will be created in the output dir with the following naming convention:

s00002c00004c00005 (scaffold, left contig, right contig)

Within each subproject directory is a scaffInfo file with the following tab-delimited one line format:

 1.Gap Name          ex. s00002c00009c00004
 2.Gap Size          ex. 100
 3.Left Contig Len   ex. 548
 4.Left Contig Name  ex. contig00009
 5.Right Contig Len  ex. 19097
 6.Right Contig Name ex. contig00004
 7.Scaffold          ex. scaffold00002

Parameters required on the command line are :

 -rl = minReadLinkage = minimum reads linking two contigs
                        required to create subproject
 -ms = minScaffSize   = minimum scaffold size to consider
                        when creating subprojects (kbp)
 -ic = ignoreCircGap  = if set to 0 will create an additional
                        circularization gap per scaffold if 
                        linking criteria is met.

VERSION

$Revision: 1.6 $

$Date: 2009-08-26 17:18:14 $

HISTORY