#!/bin/sh
# process_human_RMout : Processes lines matching LTR-elements in a RepeatMasker annotation (.out file) of a human sequence
#                       for re-annotation with REannotate.
#                       Required command line argument is the RepeatMasker annotation file
 
if [ $# -ne 1 ]; then
    echo "Usage: $0 <RepeatMasker annotation (.out) file>" >&2
    exit 1
fi
sed -e 's/_ / /' -e 's/-int /_I /' -e 's/\(MER[[:alnum:]]*\)\( .*LTR\/.*\)$/\1_LTR\2/' -e 's/\([^_]LTR[[:alnum:]]*\)\( .*LTR\/.*\)$/\1_LTR\2/' -e 's/\([^\/]ERV[[:alnum:]-]*\)\( .*LTR\/.*\)$/\1_I\2/' -e 's/\([Hh][Aa][Rr][Ll][Ee][Qq][Uu][Ii][Nn]\)/\1_I/' -e 's/\(MLT[12][[:alnum:]]*\) \(.*LTR\/.*\)$/\1_LTR \2/' -e 's/PRIMA4_LTR_I/PRIMA4_I/' -e 's/\(PABL_[AB]\) /\1_LTR /' -e 's/\(LOR1[ab]\) /\1_LTR /' -e 's/\(THE[[:alnum:]]*\) \(.*LTR\/.*\)$/\1_LTR \2/' -e 's/\(MST[[:alnum:]]*\) \(.*LTR\/.*\)$/\1_LTR \2/' -e 's/HRES1 \(.*\)$/HRES1_I \1/' -e 's/\(HUERS[[:alnum:]-]*\) /\1_I /' -e 's/LTR5_Hs /LTR5_Hs_LTR /' < $1 > processed_$1