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

Perl module object sequence bioperl Bioperl object sequence packaging

Bio::Seq::SeqWithQuality Description

Bio::Seq::SeqWithQuality is a Bioperl object packaging a sequence with its quality. 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); Requirements: · Perl

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