Difference between revisions of "PhyloSoC:BioPerl integration of the NeXML exchange standard and Bio::Phylo toolkit/nexml module design"

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m (Nexml Item Module Design (work in progress))
m (Nexml Item Module Design (work in progress))
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==== Overview ====
 
==== Overview ====
  
Currently, parsing a nexml file into Bioperl makes use of the *IO modules (AlignIO, SeqIO, and TreeIO) to load nexml represented data into bioperl objects.  These modules will handle each data type separately, but the ultimate goal is to make this easier on the user and allow the full parsing of a nexml file with one pass of the Bio::Phylo parser without forcing the user to parse the file three times - once each for sequences, alignments, and trees. To accomplish this, a Bio::nexml module will be created that will act as a container for three different data types it contains.  A powerful feature of nexml is it's ability to relate data to each other in relevant ways. This module will also maintain (as much as possible) the relationships between data.
+
Currently, parsing a nexml file into Bioperl makes use of the *IO modules (AlignIO, SeqIO, and TreeIO) to load nexml represented data into Bioperl objects.  These modules will handle each data type separately, but the ultimate goal is to make this easier on the user and allow the full parsing of a nexml document with one pass of the Bio::Phylo parser without forcing the user to parse the file three times - once each for sequences, alignments, and trees. To accomplish this, a Bio::Nexml module will be created that will act as a container for the different Bioperl that are being used to represent an entire Nexml document.  A powerful feature of nexml is it's ability to relate data to each other in relevant ways. This module will also maintain (as much as possible) the relationships between data.
  
 
==== Data Relationships to Maintain ====
 
==== Data Relationships to Maintain ====

Revision as of 08:49, 10 June 2009

Nexml Item Module Design (work in progress)

Overview

Currently, parsing a nexml file into Bioperl makes use of the *IO modules (AlignIO, SeqIO, and TreeIO) to load nexml represented data into Bioperl objects. These modules will handle each data type separately, but the ultimate goal is to make this easier on the user and allow the full parsing of a nexml document with one pass of the Bio::Phylo parser without forcing the user to parse the file three times - once each for sequences, alignments, and trees. To accomplish this, a Bio::Nexml module will be created that will act as a container for the different Bioperl that are being used to represent an entire Nexml document. A powerful feature of nexml is it's ability to relate data to each other in relevant ways. This module will also maintain (as much as possible) the relationships between data.

Data Relationships to Maintain

  • Sequences <=> Nodes
    • How to do this?
  • Alignments <=> Trees
    • How to do this?
  • Taxa <=> Trees
    • How to do this?
  • Taxa <=> Alignments
    • How to do this?
  • Taxon <=> Node
    • How to do this?