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# CREATE CENTROMERS DATABASE (max, STARTED Mon Nov  5 2012)

# for emacs: -*- mode: sh; -*-

# got a directory full of bedGraph, bed and .fa files from kahayden@soe
# unpacked it into directory "karen"

cat << _EOF_ > centromers1.ra
taxId 00
db centromers1
scientificName Reconstructed Centromers
assemblyDate Nov 2012
assemblyLabel 01
assemblyShortLabel 01
photoCreditURL http://www.soe.ucsc.edu/people/kehayden
photoCreditName Karen Hayden
ncbiGenomeId 00000
ncbiAssemblyId repBase0 00000
ncbiAssemblyName repBase0
genBankAccessionID GCA_000
ncbiBioProject 00000
orderKey 20
mitoAcc none
fastaFiles /cluster/home/max/projects/karen/cenbrowser/karen/DYZ3.fa
fakeAgpMinContigGap 400
fakeAgpMinScaffoldGap 400
dbDbSpeciesDir other
clade other
genomeCladePriority 90
commonName Centromers 
_EOF_

makeGenomeDb.pl centromers1.ra

# fix and load monomer names
less karen/DYZ3.bed | gawk '{print $0"\tmonomer"NR}' > DYZ3.bed
hgLoadBed centromers1 monomers DYZ3.bed 

# convert to bw and add encode annotations
mkdir /cluster/data/centromers1/bw
for i in `ls karen/DYZ3.*.txt`; do name=`echo $i | cut -d. -f2`; echo $name; bedGraphToBigWig $i /cluster/data/centromers1/chrom.sizes /cluster/data/centromers1/bw/$name.bw; done
# create tracks
for i in /cluster/data/centromers1/bw/*.bw; do name=`basename $i .bw`; echo $i; hgBbiDbLink centromers1 $name $i; done
# create trackDb entries
for i in /cluster/data/centromers1/bw/*.bw; do name=`basename $i .bw`; echo track $name; echo shortLabel $name; echo longLabel $name; echo group regulation; echo type bigWig 0 13; echo parent encode; echo; done > ~/kent/src/hg/makeDb/trackDb/other/centromers1/trackDb.encode.ra