NAME

reads2fasta.pl

SYNOPSIS


  reads2fasta.pl      -pd       <phd_dir>
                      -of       <path to fasta output file>
                      -oq       <path to qual output file>
                      -help
                      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.
    If the phd file for the read exists in the phd_dir specified
    by -pd by the command line, the fasta and quals are written.
    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:
    -pd phd_dir where the phd files are kept
    -of path to output fasta file.  This file will contain 
        the fasta sequences.
    -of path to output qual file.  This file will contain 
        the quality scores.
    space separated command line arguments are the read lists.

VERSION

$Revision: 1.3 $

$Date: 2009-08-26 17:18:15 $

HISTORY