Bio::SeqIO ace
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Summary
Bio::SeqIO::ace - ace sequence input/output stream
Package variables
Privates (from "my" definitions)
%bio_mol_type = ( 'dna' => 'dna', 'peptide' => 'protein', )
Included modules
Bio::Seq
Bio::Seq::SeqFactory
Inherit
Bio::SeqIO
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 ace file format. It only parses a DNA or
Peptide objects contained in the ace file,
producing PrimarySeq objects from them. All
other objects in the files will be ignored. It
doesn't attempt to parse any annotation attatched
to the containing Sequence or Protein objects,
which would probably be impossible, since
everyone's ACeDB schema can be different.
It won't parse ace files containing Timestamps
correctly either. This can easily be added if
considered necessary.
Methods
_initialize
No description
Code
next_seqDescriptionCode
write_seqDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args : NONE
write_seqcodeprevnextTop
 Title   : write_seq
Usage : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq object(s)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
  my($self,@args) = @_;
  $self->SUPER::_initialize(@args);
  if( ! defined $self->sequence_factory ) {
      $self->sequence_factory(Bio::Seq::SeqFactory->new(-verbose => $self->verbose(), -type => 'Bio::PrimarySeq'));
  }
}
next_seqdescriptionprevnextTop
sub next_seq {
        my( $self ) = @_;
        local $/ = "";  # Split input on blank lines
my $fh = $self->_filehandle; my( $type, $id ); while (<$fh>) { if (($type, $id) = /^(DNA|Peptide)[\s:]+(.+?)\s*\n/si) { s/^.+$//m; # Remove first line
s/\s+//g; # Remove whitespace
last; } } # Return if there weren't any DNA or peptide objects
return unless $type; # Choose the molecule type
my $mol_type = $bio_mol_type{lc $type} or $self->throw("Can't get Bio::Seq molecule type for '$type'"); # Remove quotes from $id
$id =~ s/^"|"$//g; # Un-escape forward slashes, double quotes, percent signs,
# semi-colons, tabs, and backslashes (if you're mad enough
# to have any of these as part of object names in your acedb
# database).
$id =~ s/\\([\/"%;\t\\])/$1/g; #"
# Called as next_seq(), so give back a Bio::Seq
return $self->sequence_factory->create( -seq => $_, -primary_id => $id, -display_id => $id, -alphabet => $mol_type, ); }
}
write_seqdescriptionprevnextTop
sub write_seq {
    my ($self, @seq) = @_;

    foreach my $seq (@seq) {
	$self->throw("Did not provide a valid Bio::PrimarySeqI object")
	    unless defined $seq && ref($seq) && $seq->isa('Bio::PrimarySeqI');
        my $mol_type = $seq->alphabet;
        my $id = $seq->display_id;

        # Escape special charachers in id
$id =~ s/([\/"%;\t\\])/\\$1/g; #"
# Print header for DNA or Protein object
if ($mol_type eq 'dna') { $self->_print( qq{\nSequence : "$id"\nDNA "$id"\n}, qq{\nDNA : "$id"\n}, ); } elsif ($mol_type eq 'protein') { $self->_print( qq{\nProtein : "$id"\nPeptide "$id"\n}, qq{\nPeptide : "$id"\n}, ); } else { $self->throw("Don't know how to produce ACeDB output for '$mol_type'"); } # Print the sequence
my $str = $seq->seq; my( $formatted_seq ); while ($str =~ /(.{1,60})/g) { $formatted_seq .= "$1\n"; } $self->_print($formatted_seq, "\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return 1; } 1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHORS - James GilbertTop
Email: jgrg@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _