NAME

  cx-chaos2chadoxml.pl

SYNOPSIS

  cx-chaos2chadoxml.pl CG10833.chaos-xml > CG10833.with-macros.chaos-xml
  cx-chaos2chadoxml.pl -x CG10833.chaos-xml > CG10833.expanded.chaos-xml

DESCRIPTION

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 uses some macros.

As an optional second step, the macros are expanded to their full form (this is required for input to some programs, eg apollo)

Both steps happen via the use of XSL Stylesheet Transforms

ARGUMENTS

-x

Expand all macros to full form

-m

Create macros

REQUIREMENTS

You need an XSLT Processor, such as xsltproc, available as part of libxslt