NAME

BS_ChromosomeSplicer.pl

VERSION

Version 2.00

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:

-C,   --CHROMOSOME : The chromosome to be modified
-E,   --EDITOR : The person responsible for the edits
-M,   --MEMO : Justification for the edits
-A,   --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:

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