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Copy pathprepare_genome_mysql_chrUn.sh
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prepare_genome_mysql_chrUn.sh
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for speDir in `ls -d batsGenome/[[:lower:]]*[[:upper:]]*`
#--------------------------------------------------
# for speDir in `ls -d batsGenome/eonSpe`
#--------------------------------------------------
do
id="`basename $speDir`1"
genomic=`basename $speDir/$id.fa`
# if [ $id == "eidHel2" ]; then
# continue
# fi
#--------------------------------------------------
mskDir="$speDir/$id.mask1"
chrDir="$speDir/$id.chrs1"
trfDir="$speDir/$id.trf1"
nibDir="$speDir/$id.nib1"
lavDir="$speDir/$id.lav1"
pslDir="$speDir/$id.psl1"
chainDir="$speDir/$id.chain1"
#--------------------------------------------------
# rm -rf $chrDir $trfDir $nibDir $lavDir $pslDir $chainDir
#--------------------------------------------------
if [ ! -e $chrDir ]; then mkdir $chrDir; fi
if [ ! -e $trfDir ]; then mkdir $trfDir; fi
if [ ! -e $nibDir ]; then mkdir $nibDir; fi
if [ ! -e $mskDir ]; then mkdir $mskDir; fi
if [ ! -e $lavDir ]; then mkdir $lavDir; fi
if [ ! -e $pslDir ]; then mkdir $pslDir; fi
if [ ! -e $chainDir ]; then mkdir $chainDir; fi
maskedGenomic=`ls $mskDir/$genomic.masked`
# qsub -N $id -pe smp 16 $HOME/software/src/RepeatMasker/RepeatMasker -pa 16 -s -norna -species mammal -dir $mskDir $speDir/$genomic
# prepare mysql tables
#--------------------------------------------------
# faSize $maskedGenomic -detailed > $speDir/$id.chrom.sizes
# faSplit byName $maskedGenomic $chrDir/
#--------------------------------------------------
echo "faSplit byName $maskedGenomic $chrDir/" > $id.sh
#--------------------------------------------------
# awk -v id=$id '{printf "%s\t%d\t/synology/gbdb/%s/%s.2bit\n", $1, $2, id, id}' $speDir/$id.chrom.sizes > $speDir/$id.chromInfo.tab
# hgFakeAgp -minContigGap=1 $maskedGenomic $speDir/$id.fake.agp
# faToTwoBit $maskedGenomic $speDir/$id.2bit
#--------------------------------------------------
echo "for i in \`find $chrDir -name '*.fa'\`" >> $id.sh
echo "do" >> $id.sh
echo "curChr=\`basename \$i .fa\`" >> $id.sh
echo "trfBig -bedAt=$trfDir/\$curChr.bed -tempDir=$trfDir \$i $trfDir/\$curChr.fa" >> $id.sh
echo "faToNib $trfDir/\$curChr.fa $nibDir/\$curChr.nib" >> $id.sh
echo "done" >> $id.sh
#--------------------------------------------------
# find $trfDir -name "*.bed" | xargs cat > $speDir/$id.simplerepeat.bed
#--------------------------------------------------
# load into mysql
#--------------------------------------------------
# mkdir /synology/gbdb/$id
# faToTwoBit $speDir/$genomic /synology/gbdb/$id/$id.2bit
# hgsql -e "create database $id;"
# hgsql $id < /home/gmswenm/software/src/kentUtils/src/hg/lib/grp.sql
#--------------------------------------------------
#--------------------------------------------------
# echo "hgLoadSqlTab $id chromInfo $HOME/software/src/kentUtils/src/hg/lib/chromInfo.sql $speDir/$id.chromInfo.tab"
# hgLoadSqlTab $id chromInfo $HOME/software/src/kentUtils/src/hg/lib/chromInfo.sql $speDir/$id.chromInfo.tab
# hgGoldGapGl $id $speDir/$id.fake.agp
# hgLoadBed $id simpleRepeat $speDir/$id.simplerepeat.bed -sqlTable=./kentUtils/src/hg/lib/simpleRepeat.sql
# hgLoadOut $id $mskDir/$genomic.out
#--------------------------------------------------
done