README

Karyotype Parser

This is based on the ISCN defined language.  However, most karyotypes do not conform perfectly and there are still errors in checking the formulas.
A logger is not required but is recommended due to the large number of unhandled parser errors currently.  See bin/ex_karyotype.rb for example use with logger and example karyotypes.

NOTE: This is currently only set up for human karyotypes.  Ploidy calculation is currently based on the human haplotype (23) and human sex chromosomes (XX/XY). The chromosome bands are
defined in the resources file and currently hardcoded.  For use with other organisms these would need to be changed and tested.

Use:

require 'cytogenetics'
require 'logger'

log = Logger.new("test.txt")
log.datetime_format = "%M"
log.level = Logger::INFO
Cytogenetics.logger = log


kt = Cytogenetics.karyotype(<<karyotype string>>)
kt.report_breakpoints
kt.report_fragments
kt.summarize