Bio::Gonzales::Seq - Gonzales Sequence Object
my $seq = Bio::Gonzales::Seq->new(id => $id, seq => $seq, desc? => '', delim? => ' '); print $seq->def; print $seq->desc;
The description of a sequence object. In case of FASTA-files, this corresponds to the text after the first space.
An hash of additional stuff you can store about the sequence
The definition also known as the FASTA header line w/o ">"
Clone the sequence
Clone the sequence properties, do not clone the sequence string.
Same as $seq-id>
$seq-
The complete sequence in fasta format, ready to be written.
The complete sequence in pretty fasta format, ready to be written.
Return a Bio::PrimarySeqI compatible object, so you can use it in BioPerl.
Create the reverse complement of the sequence. THIS FUNCTION ALTERS THE SEQUENCE OBJECT.
Gets a subseq from $seq. Config options can be:
$seq
%c = ( keep_id => 1, # keeps the original id of the sequence attach_details => 1, # keeps the original range and strand in $seq->info->{subseq} wrap => 1, # see further down relaxed_range => 1, # substitute 0 or undef for $begin with '^' and for $end with '$' relaxed_revcom => 1, # substitute N for all characters that are non-AGCTN before doing a reverse complement );
There are several possibilities for $begin and $end:
$begin
$end
GGCAAAGGA ATGATGGTGT GCAGGCTTGG CATGGGAGAC ^..........^ (1,11) OR ('^', 11) ^.....................................^ (4,'$') ^..............^ (21,35) { with wrap on: OR (-19,35) OR (-19, -5) } ^..................^ (21,35) { with wrap on: OR (-19,'$') }
wrap
The default is to limit all negative values to the sequence boundaries, so a negative begin would be equal to 1 or '^' and a negative end would be equal to '$'.
See also "fasubseq" in Bio::Gonzales::Seq::IO.
Stolen from Bio::Perl. Alphabet can be 'rna' or 'dna';
jw bargsten, <joachim.bargsten at wur.nl>
<joachim.bargsten at wur.nl>
To install Bio::Gonzales, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Gonzales
CPAN shell
perl -MCPAN -e shell install Bio::Gonzales
For more information on module installation, please visit the detailed CPAN module installation guide.