Bio::Seq::SeqWithQuality 1.4

Bio::Seq::SeqWithQuality is a Bioperl object packaging a sequence with its quality.

SYNOPSIS

use Bio::PrimarySeq;
use Bio::Seq::PrimaryQual;

# make from memory
my $qual = Bio::Seq::SeqWithQuality->new
( -qual => '10 20 30 40 50 50 20 10',
-seq => 'ATCGATCG',
-id => 'human_id',
-accession_number => 'AL000012',
);

# make from objects
# first, make a PrimarySeq object
my $seqobj = Bio::PrimarySeq->new
( -seq => 'atcgatcg',
-id => 'GeneFragment-12',
-accession_number => 'X78121',
-alphabet => 'dna'
);

# now make a PrimaryQual object
my $qualobj = Bio::Seq::PrimaryQual->new
( -qual => '10 20 30 40 50 50 20 10',
-id => 'GeneFragment-12',
-accession_number => 'X78121',
-alphabet => 'dna'
);

# now make the SeqWithQuality object
my $swqobj = Bio::Seq::SeqWithQuality->new
( -seq => $seqobj,
-qual => $qualobj
);
# done!

$swqobj->id(); # the id of the SeqWithQuality object
# may not match the the id of the sequence or
# of the quality (check the pod, luke)
$swqobj->seq(); # the sequence of the SeqWithQuality object
$swqobj->qual(); # the quality of the SeqWithQuality object

# to get out parts of the sequence.

print "Sequence ", $seqobj->id(), " with accession ",
$seqobj->accession, " and desc ", $seqobj->desc, "n";

$string2 = $seqobj->subseq(1,40);

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Requirements:

· Perl