NAME

BS_ChromosomeCutter.pl

VERSION

Version 2.10

DESCRIPTION

This utility removes features from a chromosome and offers the chance to
  replace them with custom features. Custom features should be defined in
  config/features.txt. You must define a sequence segment for the edits;it
  can be the entire chromosome.

The utility can be run in four modes:
  seqdel - The defined sequence segment will be deleted. You can have a
    custom feature inserted in its place.
  seqdelprp - A deletion proposal feature that spans the defined sequence
    segment will be created.  No sequence editing will take place.
  featdel - All features of the target type in the defined sequence segment
    will be deleted. You can have a custom feature inserted in their place.
  featdelprp - Deletion proposal features that span each feature of the target
    type in the defined sequence segment will be created. No sequence editing
    will take place.
  listdel - You provide a list of feature names; all of those features will be
    deleted.

ARGUMENTS

Required arguments:

--CHROMOSOME : The chromosome to be modified
--EDITOR : The person responsible for the edits
--MEMO : Justification for the edits
--ACTION : The action to take.
      seqdel : delete the defined segment
      seqdelprp : propose the defined segment for deletion
      featdel : delete features of type -T from the defined segment
                requires -T
      featdelprp : propose features of type -T for deletion
                requires -T
      listdel : delete the features listed in -F
                requires -F

Optional arguments:

--STARTPOS : The first base eligible for editing (default 1)
--STOPPOS : The last base eligible for editing (default chr length)
--ITERATE : [genome, chromosome (def)] Which version number to increment?
--TYPE : The type of feature to be targeted
--DESTROY : Whether or not other features should be disrupted by
    insertions; default 0 for no
--FEATURES : A comma separated list of feature names to be deleted
--INSERT : The feature to be inserted in each deletion;
           must be an entry in config/features.txt
--OUTPUT : html or txt
-h,   --help : Display this message