Bio::Chaos - utility class for handling Chaos-XML River stage zero No dependents

This module contains some basic methods for manipulating a Chaos-XML document stored in memory as a Data::Stag tree. This class is fairly minimal. One of the principal ideas being Bio::Chaos is that access to the data model should be directly through...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Root - root utility class for chaos objects River stage zero No dependents

Root class for chaos objects this class inherits from Bio::Root::Root, so you get all that juicy stuff too INHERITANCE Bio::Root::Root...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::DB::Chado - I/O from a chado db River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::XSLTHelper - chains xslts River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::ChaosGraph - object for representing a chaos-xml dataset River stage zero No dependents

This class allows manipulation of in-memory Chaos documents as Data::Stag nodes, and provides additional methods for traversing the graph structure defined in the Chaos document...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::FeatureUtil - sequence and feature utilities River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Parser::gff3 - gff sequence input/output stream River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Parser::fasta - fasta sequence input/output stream River stage zero No dependents

generates events with this schema: (fastaseqset (fastaseq* (header "str") (residues "str") (seqlen "int")))...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Parser::base_parser - DESCRIPTION of Object River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Handler::base_handler - DESCRIPTION of Object River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

Bio::Chaos::Handler::gff3_to_chaos River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-query-chado.pl River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-chadoxml2chaos.pl River stage zero No dependents

Converts Chado-XML to Chaos-XML Note that there are different "flavours" of Chado-XML. This includes both macro-ified and un-macroified flavours. This script will handle both As a first step, this script will expand all macros in the the input file t...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-chadoxml2chaos.pl River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-chaos2chadoxml.pl River stage zero No dependents

Converts Chaos-XML to Chado-XML Note that there are different "flavours" of Chado-XML. This includes both macro-ified and un-macroified flavours. This script will handle both As a first step, the chaos-xml is converted to chado-xml; this chado-xml us...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-chadoxml2chaos.pl River stage zero No dependents

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-chaos2chadoxml.pl River stage zero No dependents

Converts Chaos-XML to Chado-XML Note that there are different "flavours" of Chado-XML. This includes both macro-ified and un-macroified flavours. This script will handle both As a first step, the chaos-xml is converted to chado-xml; this chado-xml us...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-genbank2chaos.pl.pl River stage zero No dependents

Converts a genbank file to a chaos xml file (or a collection of chaos xml files). The genbank file is 'unflattened' in order to infer the relationships between features with the -islands option set, this loops through a list of genbank-formatted file...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

cx-genbank2chaos.pl.pl River stage zero No dependents

Converts a genbank file to a chaos xml file (or a collection of chaos xml files). The genbank file is 'unflattened' in order to infer the relationships between features with the -islands option set, this loops through a list of genbank-formatted file...

CMUNGALL/Bio-Chaos-0.02 - 02 Sep 2005 18:47:08 UTC

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