Perl extensions for dealing with molecular sequence data formats (FASTA, FASTQ, GFF3, and more)
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lib/JFR
scripts
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LICENSE
MANIFEST
Makefile.PL
README

README

JFR-PerlModules
======

Perl extensions for dealing with molecular sequence data

MODULES
------------

JFR::Fasta - module to parse FASTA-formatted files
JFR::Fastq - module to parse FASTQ-formatted files
JFR::FormatSeq - module to format the printing of sequences
JFR::GFF3 - module to parse GFF3-formatted files
JFR::Translate - module to translate DNA and RNA sequences

SCRIPTS
-------

See scripts directory for examples using modules. Scripts are installed automaticaly if using standard install outlined below.

INSTALLATION
------------

To install these modules and scripts type the following:

   perl Makefile.PL
   make
   make test
   make install
   
To install without root privelages try:

   perl Makefile.PL PREFIX=/home/myuser/scripts
   make
   make test
   make install

   # NOTE: A user reported receiving this message: "Only one of PREFIX or INSTALL_BASE can be given. Not both"
   # The fix was: perl Makefile.PL INSTALL_BASE=/home/myuser/scripts
   
   # to use these modules on non-root installations add to top of script(s):
   # use lib qw(/home/myuser/scripts/perl5); 
   # this should be the directory that contains the JFR directory after 'make install'

HELP
------------

Detailed documentation is embedded in each module and script in the form of pod (plain old documentation). It can be viewed by using the perldoc program

    perldoc JFR::Fasta
    perldoc JFR::Fastq
    perldoc JFR::FormatSeq
    perldoc JFR::GFF3
    perldoc JFR::Translate
    perldoc fasta2phy.pl

SYNOPSIS
------------

    use JFR::Fasta;
    my $fp = JFR::Fasta->new($fasta_file);
    while (my $rec = $fp->get_record()) {
        print "$rec->{'def'}\n";
        print "$rec->{'seq'}\n";
        my $id = JFR::Fasta->get_def_w_o_gt($rec->{'def'});
    }

    use JFR::Fastq;
    my $fq = JFR::Fastq->new($fastq_file);
    while (my $rec = $fq->get_record()) {
        print "$rec->{'def'}\n";
        print "$rec->{'rest'}\n";
        # or
        $fq->print_record();
    }

see embedded perldoc documenation for more examples

COPYRIGHT AND LICENCE
------------

Copyright (C) 2014 by Joseph Ryan

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program in the file LICENSE.  If not, see
http://www.gnu.org/licenses/.