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]\n",
$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://github.com/bioperl/bioperl-live/issues
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