NAME

BS_ChromosomeSplicer.pl

VERSION

Version 2.10

DESCRIPTION

This utility inserts features into a chromosome. 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 three modes:
  segmentflank - In this mode, a custom feature will be inserted at both
    ends of the defined sequence segment. The insert will interrupt any
    feature that overlaps the segment edges.
  featflank - In this mode, all instances of a feature in the defined sequence
    segment will be flanked (3', 5', or both) at a defined distance with an
    instance of a custom feature. This insertion will NOT interrupt any
    features;if a target feature cannot be flanked without interrupting
    another chromosomal feature, you will be informed.
  featins - In this mode, a custom feature will be inserted at the five prime
    end of the defined sequence segment. You must give the feature a unique
    name.

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.
   segmentflank : flank the defined segment with custom features
           requires -I
   featflank : flank a feature type in the defined segment with
           custom features;requires -I, -F, -DIS, -DIR
   featins : insert a custom feature at the five prime end of the
                  defined segment;requires -I, -N

Optional arguments:

--ITERATE : [genome, chromosome (def)] Which version number to increment?
--STARTPOS : The first base eligible for editing, defaults to 1
--STOPPOS : The last base eligible for editing, defaults to chr length
--DESTROY : Whether or not other features should be disrupted by
    insertions; default 0 for no
--FEATURE : The feature to be targeted
--INSERT : The custom feature to be inserted;must be an entry in
    config/features.txt
--DISTANCE : The distance in base pairs from a feature for an
    insertion; required for action featflank
--DIRECTION : [3, 5, 35] Should custom features be inserted 3p, 5p, or
    both 3p and 5p of a feature;required for action featflank
--NAME : What to name the inserted feature;required for action featins
--OUTPUT : [html, txt (def)] Format for reporting and output
-h,   --help : Display this message