NAME

matrix_gen.pl

SYNOPSIS

    matrix_gen.pl -psid -c conf/example.conf -o outfile.matrix

DESCRIPTION

This helper script builds frequency matrices for you in GENDIST format given a list of strains supplied in a TURNIP conf file.

USAGE

    Builds a frequency matrix for you in GENDIST format given a list of strains supplied in a TURNIP conf file.
    Unfortunately cannot deal with COMPLEX polymorphisms yet!

    usage: matrix_gen.pl [-hpsid] [-c config_file] [-o output_file]

     -h        : this (help) message
     -p        : include pSNP frequencies
     -s        : include SNP frequencies
     -i        : include insertion frequencies
     -d        : include deletion frequencies
     -c        : config file to use
     -o        : optional output matrix filename

    e.g.

    - build a matrix of pSNP frequencies and write to specified outfile:
    matrix_gen.pl -p -c conf/example.conf -o psnp.out.matrix

    - build a matrix of pSNP variation frequencies and output to default (psnp.matrix):
    matrix_gen.pl -p -c conf/example.conf

    - build a matrix of all variation frequencies and output to default (all.matrix):
    matrix_gen.pl -psid -c conf/example.conf

FEEDBACK

Reporting Bugs

Please report bugs to the author.

AUTHOR

Rob Davey