Genome annotation

cegma_snap_train.sh

#=============================================================================
#     FileName: cegma_train.sh
#         Desc: A short script for training a cegma annotation for SNP hmm set!
#       Author: tanhao
#        Email: tanhao2013@gmail.com
#     HomePage: http://buttonwood.github.io
#      Version: 0.0.1
#   LastChange: 2014-03-21 10:13:08
#      History:
#=============================================================================

if [ $# != 2 ];then
    echo "sh $0 cegma.gff genome.fa";
    exit;
fi
gff=`basename $1`
ref=`basename $2`
odr=`pwd`

SNP_BIN="/data/tanhao/dev/gene_prediction/denovo/snap"
MAKER_BIN="/data/tanhao/dev/gene_prediction/MAKER/maker/src/bin"

mkdir 0.Trainning
mkdir 1.SNP
date
cd 0.Trainning
echo "$MAKER_BIN/cegma2zff $odr/$gff $odr/$ref;"
$MAKER_BIN/cegma2zff $odr/$gff $odr/$ref;
echo "$SNP_BIN/fathom genome.ann genome.dna -categorize 1000;"
$SNP_BIN/fathom genome.ann genome.dna -categorize 1000;
echo "$SNP_BIN/fathom -export 1000 -plus uni.ann uni.dna;"
$SNP_BIN/fathom -export 1000 -plus uni.ann uni.dna;
echo "$SNP_BIN/forge export.ann export.dna;"
$SNP_BIN/forge export.ann export.dna;
echo "$SNP_BIN/hmm-assembler.pl $odr/$ref . > $ref.cegmasnap.hmm;"
$SNP_BIN/hmm-assembler.pl $odr/$ref . > $ref.cegmasnap.hmm;
date
echo "Trainning Done!"
cd ../1.SNP
echo "$SNP_BIN/snap $odr/0.Trainning/$ref.cegmasnap.hmm $odr/$ref -gff >snap.gff;"
$SNP_BIN/snap $odr/0.Trainning/$ref.cegmasnap.hmm $odr/$ref -gff >snap.gff;
cd ../
date
echo "SNPA Done!"