ABI
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my @trace_g = $abi->get_trace("G"); # Get the raw traces for "G"
my @base_calls = $abi->get_base_calls(); # Get the base calls
=head1 DESCRIPTION
An ABI chromatogram file is in binary format. It contain several
information only some of which is required for normal use. This
module only gives access to the most used information stored in
ABI file. All the accesses are read only.
If you have edited the file using a trace editor, then you can use the corresponding
method to access the edited sequence and base calls.
=head1 CONSTRUCTOR
=head2 new()
Usage : $abi = ABI->new(-file=>"filename");
$abi = ABI->new("filename"); # same thing
=head1 AUTHOR
Malay <malay@bioinformatics.org>
=head1 BUGS
Please report any bugs or feature requests to
C<bug-abi at rt.cpan.org>, or through the web interface at
L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=ABI>.
I will be notified, and then you'll automatically be notified of progress on
your bug as I make changes.
or
You can directly contact me to my email address.
=head1 SUPPORT
You can find documentation for this module with the perldoc command.
perldoc ABI
You can also look for information at:
=item * Search CPAN
L<http://search.cpan.org/dist/ABI>
=back
=head1 COPYRIGHT & LICENSE
Copyright 2002,2006 Malay, all rights reserved.
This program is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
=cut
1;
use strict;
use warnings;
use Module::Build;
use Module::Build::Compat;
my $build = Module::Build->new(
module_name => 'ABI',
license => 'perl',
dist_author => 'Malay <malay@bioinformatics.org>',
dist_version_from => 'ABI.pm',
build_requires =>{
'Test::More' =>0,
},
add_to_cleanup => ['ABI-*'],
create_makefile_pl => 'traditional',
);
$build->create_build_script();
Module::Build::Compat->create_makefile_pl('traditional', $build);
and so on. (You will not be required to justify it to the
Copyright Holder, but only to the computing community at large
as a market that must bear the fee.)
"Freely Available" means that no fee is charged for the item
itself, though there may be fees involved in handling the item.
It also means that recipients of the item may redistribute it
under the same conditions they received it.
1. You may make and give away verbatim copies of the source form of the
Standard Version of this Package without restriction, provided that you
duplicate all of the original copyright notices and associated disclaimers.
2. You may apply bug fixes, portability fixes and other modifications
derived from the Public Domain or from the Copyright Holder. A Package
modified in such a way shall still be considered the Standard Version.
3. You may otherwise modify your copy of this Package in any way, provided
that you insert a prominent notice in each changed file stating how and
when you changed that file, and provided that you do at least ONE of the
following:
interpreter is so embedded.
6. The scripts and library files supplied as input to or produced as
output from the programs of this Package do not automatically fall
under the copyright of this Package, but belong to whoever generated
them, and may be sold commercially, and may be aggregated with this
Package. If such scripts or library files are aggregated with this
Package via the so-called "undump" or "unexec" methods of producing a
binary executable image, then distribution of such an image shall
neither be construed as a distribution of this Package nor shall it
fall under the restrictions of Paragraphs 3 and 4, provided that you do
not represent such an executable image as a Standard Version of this
Package.
7. C subroutines (or comparably compiled subroutines in other
languages) supplied by you and linked into this Package in order to
emulate subroutines and variables of the language defined by this
Package shall not be considered part of this Package, but are the
equivalent of input as in Paragraph 6, provided these subroutines do
not change the language in any way that would cause it to fail the
regression tests for the language.
8. Aggregation of this Package with a commercial distribution is always
permitted provided that the use of this Package is embedded; that is,
when no overt attempt is made to make this Package's interfaces visible
to the end user of the commercial distribution. Such use shall not be
construed as a distribution of this Package.
9. The name of the Copyright Holder may not be used to endorse or promote
products derived from this software without specific prior written permission.
name: ABI
version: 1.0
author:
- 'Malay <malay@bioinformatics.org>'
abstract: |-
Perl module to parse chromatogram files generated by
Applied Biosystems (ABI) automated DNA sequencing machine.
by Malay K Basu (malay@bioinformatics.org); source code available at:
http://search.cpan.org/~malay
license: perl
resources:
license: http://dev.perl.org/licenses/
build_requires:
Test::More: 0
generated_by: Module::Build version 0.2805
meta-spec:
url: http://module-build.sourceforge.net/META-spec-v1.2.html
version: 1.2
- or -
perl Build.PL
./Build
./Build test
./Build install
DEPENDENCIES
This module requires Test::More
COPYRIGHT AND LICENCE
Copyright (C) 2002,2006 Malay Kumar Basu <malay@bioinformatics.org>
This module is distributed under Perl artistic license. See "License" file
for details.
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