Bio::Assembly::Singlet - Perl module to hold and manipulate singlets from sequence assembly contigs.
# Module loading use Bio::Assembly::IO; # Assembly loading methods $aio = new Bio::Assembly::IO(-file=>"test.ace.1", -format=>'phrap'); $assembly = $aio->next_assembly; foreach $singlet ($assembly->all_singlets) { # do something }
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 : seq_to_singlet Usage : my $singlet = $io->seq_to_singlet($seq) Function: Wrap the information for a singlet as a Bio::Assembly::Singlet Returns : A Bio::Assembly::Singlet object Args : A Bio::Seq-compliant object
Title : id Usage : my $id = $singlet->id('chad matsalla') Function: Returns : Args :
Title : seqref Usage : my $seqref = $singlet->seqref($seq); Function: Set the sequence to which this Singlet refers Returns : A Bio::Seq-compliant object Args :
Title : chromatfilename Usage : my $chromatfilename = $singlet->chromatfilename($newfilename); Function: Get the name of the chromatfile for this singlet Returns : A string. Args : If a string is provided, the chromatfilename will be set to that value.
Title : phdfilename Usage : my $phdfilename = $singlet->phdfilename($newfilename); Function: Get the name of the phdfile for this singlet Returns : A string. Args : If a string is provided, the phdfilename will be set to that value.
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.