BioPerl script to mask a sequence

[dbolser@nanna bioperl-live]$ git status
# On branch master
# Changed but not updated:
#   (use "git add <file>..." to update what will be committed)
#
#       modified:   Bio/DB/SeqFeature/Store/DBI/mysql.pm
#       modified:   Bio/FeatureIO.pm
#       modified:   Bio/FeatureIO/gff.pm
#       modified:   scripts/Bio-SeqFeature-Store/bp_seqfeature_load.PLS
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#       Bio/ASN1/
#       Bio/FeatureIO/agp.pm
#       foo
#       mysql.pm.patch
no changes added to commit (use "git add" and/or "git commit -a")