Bio::SeqIO::chaos(3pm) User Contributed Perl Documentation Bio::SeqIO::chaos(3pm)
NAME
Bio::SeqIO::chaos - chaos sequence input/output stream
SYNOPSIS
#In general you will not want to use this module directly;
#use the chaosxml format via SeqIO
$outstream = Bio::SeqIO->new(-file => $filename,
-format => 'chaosxml');
while ( my $seq = $instream->next_seq() ) {
$outstream->write_seq($seq);
}
DESCRIPTION
This is the guts of Bio::SeqIO::chaosxml - please refer to the documentation for this module
CURRENTLY WRITE ONLY
ChaosXML is an XML mapping of the chado relational database; for more information, see http://www.fruitfly.org/chaos-xml
chaos can be represented in various syntaxes - XML, S-Expressions or indented text. You should see the relevant SeqIO file. You will
probably want to use Bio::SeqIO::chaosxml, which is a wrapper to this module.
USING STAG OBJECTS
non-standard bioperl stuff you don't necessarily need to know follows
This module (in write mode) is an event producer - it generates XML events via the Data::Stag module. If you only care about the final end-
product xml, use Bio::SeqIO::chaosxml
You can treat the resulting chaos-xml stream as stag XML objects;
$outstream = Bio::SeqIO->new(-file => $filename, -format => 'chaos');
while ( my $seq = $instream->next_seq() ) {
$outstream->write_seq($seq);
}
my $chaos = $outstream->handler->stag;
# stag provides get/set methods for xml elements
# (these are chaos objects, not bioperl objects)
my @features = $chaos->get_feature;
my @feature_relationships = $chaos->get_feature_relationships;
# stag objects can be queried with functional-programming
# style queries
my @features_in_range =
$chaos->where('feature',
sub {
my $featureloc = shift->get_featureloc;
$featureloc->strand == 1 &&
$featureloc->nbeg > 10000 &&
$featureloc->nend < 20000;
});
foreach my $feature (@features_in_range) {
my $featureloc = $feature->get_featureloc;
printf "%s [%d->%d on %s]
",
$feature->sget_name,
$featureloc->sget_nbeg,
$featureloc->sget_end,
$featureloc->sget_srcfeature_id;
}
MODULES REQUIRED
Data::Stag
Downloadable from CPAN; see also http://stag.sourceforge.net
FEEDBACK
Mailing Lists
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
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 Bugs
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/
AUTHOR - Chris Mungall
Email cjm@fruitfly.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
context_namespace
Title : context_namespace
Usage : $obj->context_namespace($newval)
Function:
Example :
Returns : value of context_namespace (a scalar)
Args : on set, new value (a scalar or undef, optional)
IDs will be preceded with the context namespace
next_seq
Title : next_seq
Usage : $seq = $stream->next_seq()
Function: returns the next sequence in the stream
Returns : Bio::Seq object
Args :
write_seq
Title : write_seq
Usage : $stream->write_seq($seq)
Function: writes the $seq object (must be seq) to the stream
Returns : 1 for success and 0 for error
Args : Bio::Seq
perl v5.14.2 2012-03-02 Bio::SeqIO::chaos(3pm)