| Bio::Assembly::Singlet(3pm) | User Contributed Perl Documentation | Bio::Assembly::Singlet(3pm) |
Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
$aio = Bio::Assembly::IO->new( -file => 'test.ace.1',
-format => 'phrap' );
$assembly = $aio->next_assembly;
foreach $singlet ($assembly->all_singlets) {
# do something
}
# OR, if you want to build the singlet yourself,
use Bio::Assembly::Singlet;
$singlet = Bio::Assembly::Singlet->new(
-id => 'Singlet1',
-seqref => $seq
);
A singlet is a sequence that phrap was unable to align to any other sequences.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : $singlet = $io->new( -seqref => $seq )
Function: Create a new singlet object
Returns : A Bio::Assembly::Singlet object
Args : -seqref => Bio::Seq-compliant sequence object for the singlet
Title : seqref
Usage : $seqref = $singlet->seqref($seq);
Function: Get/set the sequence to which this singlet refers
Returns : A Bio::Seq-compliant object
Args : A Bio::Seq-compliant or Bio::Seq::Quality object
Title : _seq_to_singlet
Usage : $singlet->seqref($seq)
Function: Transform a sequence into a singlet
Returns : 1 for success
Args : A Bio::Seq-compliant object
| 2018-10-27 | perl v5.26.2 |