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# -*-Perl-*-
## Bioperl Test Harness Script for Modules
## $Id: scf.t,v 1.8 2003/01/28 23:27:05 matsallac Exp $
#
use strict;
BEGIN {
use vars qw($DEBUG $verbose);
$DEBUG = $ENV{'BIOPERLDEBUG'};
$verbose = $DEBUG ? 0 : -1;
# to handle systems with no installed Test module
# we include the t dir (where a copy of Test.pm is located)
# as a fallback
eval { require Test; };
if( $@ ) {
use lib 't';
}
use Test;
plan tests => 12;
}
END {
unlink qw(
write_scf.scf
write_scf_synthetic_traces.scf
write_scf_subtrace.scf
write_scf_version2.scf
);
}
use Dumpvalue();
my $dumper = new Dumpvalue();
$dumper->veryCompact(1);
use Bio::SeqIO::scf;
use Bio::Seq::SequenceTrace;
my $in_scf = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile("t","data",
"chad100.scf"),
'-format' => 'scf',
'-verbose' => $verbose);
ok($in_scf);
my $swq = $in_scf->next_seq();
ok (ref($swq) eq "Bio::Seq::SequenceTrace");
ok (length($swq->seq())>10);
my $qualities = join(' ',@{$swq->qual()});
ok (length($qualities)>10);
my $id = $swq->id();
ok ($swq->id() eq "ML4942R");
my $a_channel = $swq->trace("a");
ok (scalar(@$a_channel) > 10);
my $c_channel = $swq->trace("c");
ok (length($c_channel) > 10);
my $g_channel = $swq->trace("g");
ok (length($g_channel) > 10);
my $t_channel = $swq->trace("t");
ok (length($t_channel) > 10);
my $ref = $swq->peak_indices();
my @indices = @$ref;
ok (scalar(@indices), 761);
print("Now checking version3...\n");
my $in_scf_v3 = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile
("t","data",
"version3.scf"),
'-format' => 'scf',
'-verbose' => $verbose);
my $v3 = $in_scf_v3->next_seq();
my $ind = $v3->peak_indices();
my @ff = @$ind;
# print("ind is $ind which is @ff\n");
@indices = @{$v3->peak_indices()};
ok (scalar(@indices) == 1106);
# $dumper->dumpValue($v3);
# my %header = %{$in_scf_v3->get_header()};
# ok $header{bases}, 1106;
# ok $header{samples}, 14107;
print("Now testing the _writing_ of scfs\n");
my $out_scf = Bio::SeqIO->new('-file' => ">write_scf.scf",
'-format' => 'scf',
'-verbose' => $verbose);
# the new way
$out_scf->write_seq(
-target => $v3,
-MACH => 'CSM sequence-o-matic 5000',
-TPSW => 'trace processing software',
-BCSW => 'basecalling software',
-DATF => 'AM_Version=2.00',
-DATN => 'a22c.alf',
-CONV => 'Bioperl-scf.pm');
ok( -e "write_scf.scf" && ! -z "write_scf.scf" );
$out_scf = Bio::SeqIO->new('-verbose' => 1,
'-file' => ">write_scf_synthetic_traces.scf",
'-format' => 'scf');
$swq = Bio::Seq::SeqWithQuality->new(-seq=>'ATCGATCGAA',
-qual=>"10 20 30 40 50 20 10 30 40 50",
-alphabet=>'dna');
my $trace = Bio::Seq::SequenceTrace->new(
-swq => $swq);
$out_scf->write_seq(
-target => $trace,
-MACH => 'CSM sequence-o-matic 5000',
-TPSW => 'trace processing software',
-BCSW => 'basecalling software',
-DATF => 'AM_Version=2.00',
-DATN => 'a22c.alf',
-CONV => 'Bioperl-scf.pm');
print("Trying to write an scf with a subset of a real scf...\n");
$out_scf = Bio::SeqIO->new('-verbose' => 1,
'-file' => ">write_scf_subtrace.scf",
'-format' => 'scf');
$in_scf_v3 = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile
("t","data",
"version3.scf"),
'-format' => 'scf',
'-verbose' => $verbose);
$v3 = $in_scf_v3->next_seq();
# print("The full trace object is as follows:\n");
my $sub_v3 = $v3->sub_trace_object(5,50);
print("The subtrace object is this:\n");
$dumper->dumpValue($sub_v3);
$out_scf->write_seq(
-target => $sub_v3
);
my $in_scf_v2 = Bio::SeqIO->new('-file' => Bio::Root::IO->catfile
("t","data",
"version2.scf"),
'-format' => 'scf',
'-verbose' => $verbose);
$v3 = $in_scf_v2->next_seq();
$out_scf = Bio::SeqIO->new(-file => ">write_scf_version2.scf",
-format => "scf");
$out_scf->write_seq( -target => $v3,
-version => 2 );
# now some version 2 things.
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