src/hg/makeDb/doc/ferrAcid1.txt 1.3
1.3 2009/11/25 21:48:39 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/ferrAcid1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/ferrAcid1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/ferrAcid1.txt 26 Jul 2006 16:59:54 -0000 1.2
+++ src/hg/makeDb/doc/ferrAcid1.txt 25 Nov 2009 21:48:39 -0000 1.3
@@ -1,361 +1,361 @@
# for emacs: -*- mode: sh; -*-
# This file describes building the browser database for the archaeal
# species Methanosarcina acetivorans.
#
# if this is the first time you are making your own hgwdev browser, need to do
# cd ~/kent/src/, then a make
# DOWNLOAD SEQUENCE FROM GENBANK (DONE 10/2/05)
mkdir /cluster/store5/archae/ferrAcid1
ln -s /cluster/store5/archae/ferrAcid1 /cluster/data/ferrAcid1
cd /cluster/data/ferrAcid1
cp /projects/lowelab/db/Bacteria/Ferroplasma_acidarmanus/Ferr_acid* .
mv Ferr_acid.fa ferrAcid1.fa
grep ">" ferrAcid1.fa
# Edit header of ferrAcid1.fa seqs to '>chr >plasmid_pNRC100 >plasmid_pNRC200'
faToTwoBit ferrAcid1.fa ferrAcid1.2bit
mkdir /gbdb/ferrAcid1
ln -s /cluster/data/ferrAcid1/ferrAcid1.2bit /gbdb/ferrAcid1/ferrAcid1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/2/05)
ssh hgwdev
echo 'create database ferrAcid1' | hgsql ''
cd /cluster/data/ferrAcid1
faSize -detailed ferrAcid1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" | hgsql ferrAcid1
echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("ferrAcid1", "Jun 2005 Draft", "/gbdb/ferrAcid1", "Ferroplasma acidarmanus", "chr:500000-550000", 1, 280, "Ferroplasma acidarmanus","Ferroplasma acidarmanus Fer1", "/gbdb/ferrAcid1/html/description.html", 0);' | hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Ferroplasma acidarmanus", "ferrAcid1");' | hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Ferroplasma acidarmanus", "archaea",85);' | hgsql hgcentraltest
# CREATE CHROMINFO TABLE
ssh hgwdev
cd /cluster/data/ferrAcid1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql ferrAcid1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql ferrAcid1
echo "update chromInfo set fileName = '/gbdb/ferrAcid1/ferrAcid1.2bit'" | hgsql ferrAcid1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/ferrAcid1
cvs add archae/ferrAcid1
cvs commit archae/ferrAcid1
make DBS=ferrAcid1
# GC20BASE (DONE 10/2/05)
mkdir -p /cluster/data/ferrAcid1/bed/gc20Base
cd /cluster/data/ferrAcid1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -overlap=10 -win=20 ferrAcid1 /cluster/data/ferrAcid1/ | wigEncode stdin gc20Base.wig gc20Base.wib
cd /cluster/data/ferrAcid1/bed/gc20Base
mkdir /gbdb/ferrAcid1/wib
ln -s `pwd`/gc20Base.wib /gbdb/ferrAcid1/wib
hgLoadWiggle -pathPrefix=/gbdb/ferrAcid1/wib ferrAcid1 gc20Base gc20Base.wig
# verify index is correct:
hgsql ferrAcid1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE 10/2/05)
ssh hgwdev
mkdir -p /cluster/data/ferrAcid1/bed/simpleRepeat
cd /cluster/data/ferrAcid1
trfBig ferrAcid1.fa /dev/null -bedAt=/cluster/data/ferrAcid1/bed/simpleRepeat/chr.bed
cd /cluster/data/ferrAcid1/bed/simpleRepeat
hgLoadBed ferrAcid1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql
# NO TIGR GENES
# genome not available at http://www.tigr.org/tigr-scripts/CMR2/gene_attribute_form.dbi
# DESCRIPTION PAGE (DONE 10/4/05)
# Write ~/kent/src/hg/makeDb/trackDb/archae/ferrAcid1/description.html
chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/ferrAcid1/description.html
mkdir -p /cluster/data/ferrAcid1/html/
cp ~/kent/src/hg/makeDb/trackDb/archae/ferrAcid1/description.html /cluster/data/ferrAcid1/html/description.html
mkdir -p /gbdb/ferrAcid1/html
ln -s /cluster/data/ferrAcid1/html/description.html /gbdb/ferrAcid1/html/
# MULTIZ with therAcid, therVolc, picrTorr
# DONE (10/13/05), kpollard
cd /cluster/data/ferrAcid1/bed/
mkdir conservation
cd conservation
cp /cluster/data/metAce1/bed/conservation/HoxD55.q .
cp ../../chr.fa ferrAcid1.chr
sed s/Contig/ferrAcid1.Contig/ ferrAcid1.chr > temp
mv temp ferrAcid1.chr
cp /cluster/data/therAcid1/bed/conservation/therAcid1.chr .
cp /cluster/data/picrTorr1/bed/conservation/picrTorr1.chr .
cp /cluster/data/therVolc1/bed/conservation/therVolc1.chr .
faToNib therVolc1.chr therVolc1.chr.nib
faToNib therAcid1.chr therAcid1.chr.nib
faToNib picrTorr1.chr picrTorr1.chr.nib
faToTwoBit ferrAcid1.chr ferrAcid1.2bit
#chrom sizes
faSize -detailed *.chr > chrom.sizes
#make fa for each contig
faSplit byname ferrAcid1.chr ./
ls ferrAcid1.Contig*.fa > contignames.txt
cat contignames.txt | gawk '{print substr($1,11,length($1))}' > contigs.txt
foreach f (`cat contignames.txt`)
set b=$f:r
cat $f | gawk '{if(/>ferrAcid1.Contig/){print $0;}else{print toupper($0);}}' > temp
mv temp $f
faToNib $f $b.nib
end
#blastz
foreach f (`cat contignames.txt`)
set b=$f:t:r
echo $b
blastz $f therAcid1.chr Q=HoxD55.q > ${b}-therAcid1.lav
blastz $f picrTorr1.chr Q=HoxD55.q > ${b}-picrTorr1.lav
blastz $f therVolc1.chr Q=HoxD55.q > ${b}-therVolc1.lav
end
foreach f(*.lav)
set b=$f:r
echo $b
lavToAxt $f . . $b.axt
end
foreach f(`cat contignames.txt`)
set b=$f:r
echo $b
axtBest ${b}-therAcid1.axt $b -winSize=500 -minScore=5000 ${b}-therAcid1-best.axt
axtBest ${b}-picrTorr1.axt $b -winSize=500 -minScore=5000 ${b}-picrTorr1-best.axt
axtBest ${b}-therVolc1.axt $b -winSize=500 -minScore=5000 ${b}-therVolc1-best.axt
end
foreach f(*-best.axt)
set b=`basename $f -best.axt`
echo $b
axtToMaf $f chrom.sizes chrom.sizes $b.maf
end
#multiz
#remove extra header lines
foreach f(*.maf)
cat $f | gawk 'BEGIN{getline; print $0; getline; getline; getline; getline;}{print $0;}' > temp
mv temp $f
end
foreach f(`cat contignames.txt`)
set b=$f:r
echo $b
multiz ${b}-therAcid1.maf ${b}-picrTorr1.maf - > ${b}-therAcid1-picrTorr1.maf
multiz ${b}-therVolc1.maf ${b}-therAcid1-picrTorr1.maf - > ${b}-therAcid1-picrTorr1-therVolc1.maf
end
#phyloHMM
foreach f(`cat contignames.txt`)
set b=$f:r
echo $b
msa_view -i MAF -M $f -o SS ${b}-therAcid1-picrTorr1-therVolc1.maf > $b.ss
end
foreach f(`cat contigs.txt`)
set b=$f:r
cat ferrAcid1.$b.ss | gawk '{if(/^NAMES/){print "NAMES = ferrAcid1,therVolc1,therAcid1,picrTorr1";} else{print $0;}}' > temp
mv temp $b.ss
phyloFit -i SS ferrAcid1.$b.ss -t "(ferrAcid1,(picrTorr1,(therAcid1,therVolc1)))" -o ${b}_FaTaPtTv
end
#Contig 169 has the largest NTUPLES (1051) so use it for starting mod
# it shows GC=0.205868+0.188380=0.394248
#add GC content to next call
foreach f(`cat contigs.txt`)
set b=$f:r
echo $b
phastCons ferrAcid1.$b.ss Contig169_FaTaPtTv.mod \
--gc 0.3942 --target-coverage 0.7 --estimate-trees ${b} \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
end
#average with phyloBoot to get cons.mod and noncons.mod
#ls *.cons.mod > cons.txt
#phyloBoot --read-mods '*cons.txt' --output-average ave.cons.mod > cons_summary.txt
#ls *.noncons.mod > noncons.txt
#phyloBoot --read-mods '*noncons.txt' --output-average ave.noncons.mod > noncons_summary.txt
#PROBLEM: Can't do this with different numbers of species in each mod
#Again, just use Contig169 model
#get rid of SS files with no data
foreach f(`cat contignames.txt`)
set b=$f:r
wc -l $b.ss | gawk '{if($1==0){print "rm "$2}}' >> rmjobs
end
chmod +x rmjobs
rmjobs
foreach f(*.cons.mod)
set b=$f:r:r
echo $b
phastCons $b.ss Contig169.cons.mod,Contig169.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi ${b}_ferrAcid1-elements.bed --score \
--require-informative 0 --seqname $b > ${b}_cons.dat
wigEncode ${b}_cons.dat ${b}_phastCons.wig ${b}_phastCons.wib
end
#combine phastCons elements into 1 bed file
cat Contig*.bed > phastCons.bed
#move data
mkdir wib
mv Contig*_phastCons.wib wib/.
mv Contig*_phastCons.wig wib/.
ln -s /cluster/data/ferrAcid1/bed/conservation/wib/*.wib /gbdb/ferrAcid1/wib
mkdir /gbdb/ferrAcid1/pwMaf
mkdir -p otherSpp/therAcid1 otherSpp/picrTorr1 otherSpp/therVolc1
foreach f(`cat contignames.txt`)
set b=$f:r
echo $b
mv ferrAcid1.${b}-picrTorr1.maf otherSpp/picrTorr1/$b.maf
mv ferrAcid1.${b}-therAcid1.maf otherSpp/therAcid1/$b.maf
mv ferrAcid1.${b}-therVolc1.maf otherSpp/therVolc1/$b.maf
end
ln -s /cluster/data/ferrAcid1/bed/conservation/otherSpp/picrTorr1 /gbdb/ferrAcid1/pwMaf/picrTorr1_pwMaf
ln -s /cluster/data/ferrAcid1/bed/conservation/otherSpp/therVolc1 /gbdb/ferrAcid1/pwMaf/therVolc1_pwMaf
ln -s /cluster/data/ferrAcid1/bed/conservation/otherSpp/therAcid1 /gbdb/ferrAcid1/pwMaf/therAcid1_pwMaf
mkdir multiz
foreach f(`cat contignames.txt`)
set b=$f:r
echo $b
mv ferrAcid1.${b}-therAcid1-picrTorr1-therVolc1.maf multiz/$b.maf
end
ln -s /cluster/data/ferrAcid1/bed/conservation/multiz /gbdb/ferrAcid1/multizFaTaPtTv
#get rid of wig files with no data
rm rmjobs
foreach f(`cat contignames.txt`)
set b=$f:r
wc -l wib/${b}_phastCons.wig | gawk '{if($1==0){print "rm "$2}}' >> rmjobs
end
chmod +x rmjobs
rmjobs
#load
hgLoadWiggle ferrAcid1 phastCons /cluster/data/ferrAcid1/bed/conservation/wib/Contig*_phastCons.wig
hgLoadMaf -warn ferrAcid1 multizFaTaPtTv
hgLoadMaf -warn ferrAcid1 picrTorr1_pwMaf -pathPrefix=/gbdb/ferrAcid1/pwMaf/picrTorr1_pwMaf
hgLoadMaf -warn ferrAcid1 therVolc1_pwMaf -pathPrefix=/gbdb/ferrAcid1/pwMaf/therVolc1_pwMaf
hgLoadMaf -warn ferrAcid1 therAcid1_pwMaf -pathPrefix=/gbdb/ferrAcid1/pwMaf/therAcid1_pwMaf
hgLoadBed ferrAcid1 phastConsElements phastCons.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae/ferrAcid1
#trackDb.ra entry
# track multizFaTaPtTv
# shortLabel Conservation
# longLabel Methanogen multiz alignments
# group compGeno
# priority 10.0
# visibility pack
# type wigMaf 0.0 1.0
# maxHeightPixels 100:40:11
# wiggle phastCons
# yLineOnOff Off
- # autoScaleDefault Off
+ # autoScale Off
# pairwise pwMaf
# speciesOrder therAcid1 picrTorr1 therVolc1
cvs add trackDb.ra
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizFaTaPtTv.html
cvs commit -m "Details page for multiz track" multizFaTaPtTv.html
# GENBANK PROTEIN-CODING GENES ()
ssh hgwdev
mkdir /cluster/data/ferrAcid1/genbank
cd /cluster/data/ferrAcid1/genbank
cp /projects/lowelab/db/Bacteria/Ferroplasma_acidarmanus/ .
mv NC_003552.gbk ferrAcid1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > ferrAcid1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > ferrAcid1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > ferrAcid1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome ferrAcid1.gbk ferrAcid1-params-bed.txt ferrAcid1-genbank-cds.bed
gbArchaeGenome ferrAcid1.gbk ferrAcid1-params-pep.txt ferrAcid1-genbank-cds.pep
gbArchaeGenome ferrAcid1.gbk ferrAcid1-params-xra.txt ferrAcid1-genbank-cds.xra
hgLoadBed ferrAcid1 gbProtCode ferrAcid1-genbank-cds.bed
hgsql ferrAcid1 < ~/kent/src/hg/lib/pepPred.sql
hgsql ferrAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql ferrAcid1
echo rename table minGeneInfo to gbProtCodeXra | hgsql ferrAcid1
echo load data local infile \'ferrAcid1-genbank-cds.pep\' into table gbProtCodePep | hgsql ferrAcid1
echo load data local infile \'ferrAcid1-genbank-cds.xra\' into table gbProtCodeXra | hgsql ferrAcid1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' ferrAcid1-genbank-cds.bed | bedToGenePred stdin tmp.gp
tawk '{print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,substr($1,3,4),name2,"cmpl","cmpl",0}' tmp.gp > tmp2.gp
join -t " " -o 1.1,1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 2.3 1.13 1.14 1.15 tmp2.gp ferrAcid1-genbank-cds.xra > ferrAcid1.gp
# GENBANK rRNA GENES ()
ssh hgdev
cd /cluster/data/ferrAcid1/genbank
gbArchaeGenome -kind=rRNA ferrAcid1.gbk ferrAcid1-params-bed.txt ferrAcid1-rrnas.bed
echo 'gene product NA' > ferrAcid1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA ferrAcid1.gbk ferrAcid1-params-rrna-xra.txt ferrAcid1-rrnas-xra.txt
hgLoadBed ferrAcid1 gbRRNA ferrAcid1-rrnas.bed
hgsql ferrAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql ferrAcid1
echo load data local infile \'ferrAcid1-rrnas-xra.txt\' into table gbRRNAXra | hgsql ferrAcid1
# COG STUFF
# Cut and paste http://www.ncbi.nlm.nih.gov/cgi-bin/COG/palox into emacs (COG list)
# and save as cogpage.txt
awk '{printf("%s\t%s\n",$6,$5)}' < cogpage.txt | sed -e 's/\[//' -e 's/\]//' > cogs.txt
rm cogpage.txt
# Now we have the basic list of cogs and the letter code for each one.
# TODD LOWE tRNA GENES ()
# This one is a bed 6+ file created by hand of 46 tRNAs and 1 pseudo tRNA by Todd
# Lowe. See ~/kent/src/hg/lib/loweTrnaGene.as for a description of the fields.
# **Showing the tRNAScanSE instructions would be nice in the future.
ssh hgwdev
mkdir /cluster/data/ferrAcid1/bed/loweTrnaGene
cd /cluster/data/ferrAcid1/bed/loweTrnaGene
hgLoadBed -tab ferrAcid1 loweTrnaGene ferrAcid1-lowe-trnas.bed -sqlTable=~/kent/src/hg/lib/loweTrnaGene.sql
# TODD LOWE snoRNA GENES ()
# This is a bed 6 file created by hand.
ssh hgwdev
mkdir /cluster/data/ferrAcid1/bed/loweSnoGene
cd /cluster/data/ferrAcid1/bed/loweSnoGene
hgLoadBed -tab ferrAcid1 loweSnoGene ferrAcid1-snos.bed