ABI

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Changes  view on Meta::CPAN

#$Id: Changes,v 1.1.1.1.2.2 2006/11/20 03:18:12 malay Exp $

Revision history for Perl extension ABI.

1.0  Sat Nov  18  04:22:53 2006
	- Changed to Module::Build system
	- Added test data
	- Changed to Test::More
	- Access to user modified sequence
	- Access to user modified basecalls
	

0.01  Thu May  2 04:22:53 2002
	- original version; created by h2xs 1.21 with options
		-XA -n ABI

LICENSE  view on Meta::CPAN

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.

MANIFEST  view on Meta::CPAN

ABI.pm
Build.PL
Changes
LICENSE
Makefile.PL
MANIFEST			This list of files
README
t/test.t
t/TEST_modified.ab1
META.yml

README  view on Meta::CPAN

archive can use it get an idea of the modules uses. It is usually a
good idea to provide version information here so that people can
decide whether fixes for the module are worth downloading.

INSTALLATION

To install this module type the following:

   perl Makefile.PL
   make
   make test
   make install

 - 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>

t/test.t  view on Meta::CPAN

# Before `make install' is performed this script should be runnable with
# `make test'. After `make install' it should work as `perl test.pl'
#########################
# change 'tests => 1' to 'tests => last_test_to_print'
#use FindBin;
#use lib "$FindBin::Bin/..";
use Test::More qw(no_plan);

#BEGIN { plan tests => 1 };
require_ok("ABI");
my $abi = ABI->new("t/TEST_modified.ab1");
isa_ok( $abi, "ABI" );
my @base_calls = $abi->get_base_calls;

#print STDERR "@base_calls";
my @b_calls =
  qw(20 33 46 56 67 82 89 102 111 124 136 151 163 174 185 192 204 215
  225 233 246 258 274 285 297 308 324 340 349 356 369 383 393 403 413
  422 434 447 458 467 477 487 499 513 523 529 544 552 562 570 581 593

t/test.t  view on Meta::CPAN

$seq =~ s/\s//g;

is ($seq,$abi->get_corrected_sequence);

#print STDERR "\n", $abi->{_index},"\n";
#print STDERR "\n", $abi->{_seq_length_corrected},"\n";
#print "@array", "\n";

#ok(1); # If we made it this far, we're ok.
#########################
# Insert your test code below, the Test module is use()ed here so read
# its man page ( perldoc Test ) for help writing this test script.