NAME

non454Reads2Fasta.pl

SYNOPSIS


  non454Reads2Fasta.pl   -si       <sffinfo.txt file>
                         -gs       <path to gap subproject>
                         -od       <outputdir name>
                         -d        debug mode
                         -h        this help menu
                         readlistfile1 readlistfile2 ... etc
  Note:all given options are required except help

DESCRIPTION

    This script takes as input a readlist or readlist to retrieve.
    The read id to be retrieved must be in the 1st (whitespace 
    separated) column of the readlist(s) supplied on the command line.
    The non sff files specified in the -si <sffinfo.txt> file are searched
    and the fasta/quals depsited in a multi fasta file, named after the 
    input file specified in the sffinfo.txt file, in a specified output
    directory -od in the gap subproject -gs.
    The sffinfo.txt file contains the following 3 tab delim column format 
    libraryName fastaFileLocation P||U (for paired or unpaired data)
    Note: Newbler ace file information (eg. _left,_right,.pr)
          is stripped from the read id to enable use of readlists
          generated by NewblerAce2ReadPair.pl
    Options are as follows:
    -si <sffinfo.txt file>
    -gs path to gap subproject.  
    -od Output Fasta/Quals will be deposited in this directory in 
        the gap subproject directory.
    space separated command line arguments are the read lists.

VERSION

$Revision: 1.3 $

$Date: 2010-03-07 16:56:42 $

HISTORY