Bio::SeqIO
raw
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Summary
Bio::SeqIO::raw - raw sequence file input/output stream
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
Do not use this module directly. Use it via the
Bio::SeqIO class.
Description
This object can transform Bio::Seq objects to and from raw flat
file databases.
Methods
Methods description
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : |
Title : write_qual
Usage : $stream->write_qual($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object |
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Array of Bio::PrimarySeqI objects |
Methods code
sub _initialize
{ my($self,@args) = @_;
$self->SUPER::_initialize(@args);
if( ! defined $self->sequence_factory ) {
$self->sequence_factory(new Bio::Seq::SeqFactory
(-verbose => $self->verbose(),
-type => 'Bio::Seq'));
}} | sub next_seq
{ my ($self,@args) = @_;
my $nextline = $self->_readline();
if( !defined $nextline ){ return undef; }
my $sequence = uc($nextline);
$sequence =~ s/\W//g;
return $self->sequence_factory->create(-seq => $sequence); } | sub write_qual
{ my ($self,@seq) = @_;
my @qual = ();
foreach (@seq) {
unless ($_->isa("Bio::Seq::SeqWithQuality")){
warn("You cannot write raw qualities without supplying a Bio::Seq::SeqWithQuality object! You passed a ", ref($_), "\n");
next;
}
@qual = @{$_->qual};
if(scalar(@qual) == 0) {
$qual[0] = "\n";
}
$self->_print (join " ", @qual,"\n") or return;
}
return 1;
}
1;} | sub write_seq
{ my ($self,@seq) = @_;
foreach my $seq (@seq) {
$self->throw("Must provide a valid Bio::PrimarySeqI object")
unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
$self->_print($seq->seq, "\n") or return;
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;} | General documentation
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
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Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
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Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
Ewan Birney <birney@ebi.ac.uk>
Lincoln Stein <lstein@cshl.org>
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _