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