NAME
Bio::Gonzales::Seq - Gonzales Sequence Object
SYNOPSIS
my
$seq
= Bio::Gonzales::Seq->new(
id
=>
$id
,
seq
=>
$seq
, desc? =>
''
, delim? =>
' '
);
$seq
->def;
$seq
->desc;
DESCRIPTION
METHODS
- $seq->id
- $seq->desc
-
The description of a sequence object. In case of FASTA-files, this corresponds to the text after the first space.
- $seq->seq
- $seq->delim
- $seq->info
-
An hash of additional stuff you can store about the sequence
- $seq->gaps
- $seq->length
- $seq->def
-
The definition also known as the FASTA header line w/o ">"
- $seq->clone
-
Clone the sequence
- $seq->clone_empty
-
Clone the sequence properties, do not clone the sequence string.
- $seq->display_id
-
Same as
$seq-
id> - $seq->ungapped_length
- $seq->all
- "$seq"
-
The complete sequence in fasta format, ready to be written.
- $seq->all_formatted
- $seq->all_pretty
-
The complete sequence in pretty fasta format, ready to be written.
- $seq->as_primaryseq
-
Return a Bio::PrimarySeqI compatible object, so you can use it in BioPerl.
- $seq_string = $seq->gapless_seq
- $seq->rm_gaps!
- $seq->revcom
-
Create the reverse complement of the sequence. THIS FUNCTION ALTERS THE SEQUENCE OBJECT.
- $seq->subseq( [ $begin, $end, $strand , @rest ], \%c )
-
Gets a subseq from
$seq
. Config options can be:%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
: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.
- my $reverse_complement_string = Bio::Gonzales::Seq::_revcom_from_string($seq_string, $alphabet)
-
Stolen from Bio::Perl. Alphabet can be 'rna' or 'dna';
AUTHOR
jw bargsten, <joachim.bargsten at wur.nl>