src/hg/makeDb/doc/therAcid1.txt 1.3
1.3 2009/11/25 21:48:42 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/therAcid1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/therAcid1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/therAcid1.txt 26 Jul 2006 16:59:59 -0000 1.2
+++ src/hg/makeDb/doc/therAcid1.txt 25 Nov 2009 21:48:42 -0000 1.3
@@ -1,295 +1,295 @@
# 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/therAcid1
ln -s /cluster/store5/archae/therAcid1 /cluster/data/therAcid1
cd /cluster/data/therAcid1
cp /projects/lowelab/db/Bacteria/Thermoplasma_acidophilum/Ther_acid* .
mv Ther_acid.fa therAcid1.fa
grep ">" therAcid1.fa
# Edit header of therAcid1.fa seqs to '>chr >plasmid_pNRC100 >plasmid_pNRC200'
faToTwoBit therAcid1.fa therAcid1.2bit
mkdir /gbdb/therAcid1
ln -s /cluster/data/therAcid1/therAcid1.2bit /gbdb/therAcid1/therAcid1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/2/05)
ssh hgwdev
echo 'create database therAcid1' | hgsql ''
cd /cluster/data/therAcid1
faSize -detailed therAcid1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" | hgsql therAcid1
echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("therAcid1", "Sep 2000", "/gbdb/therAcid1", "Thermoplasma acidophilum", "chr:500000-550000", 1, 284, "Thermoplasma acidophilum","Thermoplasma acidophilum DSM 1728", "/gbdb/therAcid1/html/description.html", 0);' | hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Thermoplasma acidophilum", "therAcid1");' | hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Thermoplasma acidophilum", "archaea",85);' | hgsql hgcentraltest
# CREATE CHROMINFO TABLE
ssh hgwdev
cd /cluster/data/therAcid1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql therAcid1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql therAcid1
echo "update chromInfo set fileName = '/gbdb/therAcid1/therAcid1.2bit'" | hgsql therAcid1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/therAcid1
cvs add archae/therAcid1
cvs commit archae/therAcid1
make DBS=therAcid1
# GC20BASE (DONE 10/2/05)
mkdir -p /cluster/data/therAcid1/bed/gc20Base
cd /cluster/data/therAcid1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -overlap=10 -win=20 therAcid1 /cluster/data/therAcid1/ | wigEncode stdin gc20Base.wig gc20Base.wib
cd /cluster/data/therAcid1/bed/gc20Base
mkdir /gbdb/therAcid1/wib
ln -s `pwd`/gc20Base.wib /gbdb/therAcid1/wib
hgLoadWiggle -pathPrefix=/gbdb/therAcid1/wib therAcid1 gc20Base gc20Base.wig
# verify index is correct:
hgsql therAcid1 -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/therAcid1/bed/simpleRepeat
cd /cluster/data/therAcid1
trfBig therAcid1.fa /dev/null -bedAt=/cluster/data/therAcid1/bed/simpleRepeat/chr.bed
cd /cluster/data/therAcid1/bed/simpleRepeat
hgLoadBed therAcid1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql
# TIGR GENES (DONE 10/3/05)
# First go to http://www.tigr.org/tigr-scripts/CMR2/gene_attribute_form.dbi
# and fill out the web form as follows:
# - Pick "Retrieve attributes for the specified DNA feature within a specific
# organism and/or a specific role category".
# * Pick genome and "Primary and TIGR annotation ORFs"
# from the 1st and 3rd box.
# * Select everything from "Choose TIGR Annotation Gene Attributes"
# * Select "Primary Locus Name" from "Choose Primary Annotation Gene Attributes"
# * Select everything from "Choose Other Gene Attributes"
# - Click submit, and click save as tab-delimited file.
mkdir /cluster/data/therAcid1/bed/tigrCmrORFs
cp therAcid1-tigr.tab /cluster/data/therAcid1/bed/tigrCmrORFs
cd /cluster/data/therAcid1/bed/tigrCmrORFs
~aamp/bin/i386/tigrCmrToBed therAcid1-tigr.tab therAcid1-tigr.bed
cat therAcid1-tigr.bed | sed -e 's/chr1/chr/' > temp
mv temp therAcid1-tigr.bed
hgLoadBed -tab therAcid1 tigrCmrGene therAcid1-tigr.bed -sqlTable=/cluster/home/kpollard/kent/src/hg/lib/tigrCmrGene.sql
echo "rename table tigrCmrGene to tigrCmrORFs;" | hgsql therAcid1
# DESCRIPTION PAGE (DONE 10/4/05)
# Write ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html
chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html
mkdir -p /cluster/data/therAcid1/html/
cp ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html /cluster/data/therAcid1/html/description.html
mkdir -p /gbdb/therAcid1/html
ln -s /cluster/data/therAcid1/html/description.html /gbdb/therAcid1/html/
# MULTIZ with therVolc, picrTorr, and ferrAcid
# DONE (10/11/05), kpollard
cd /cluster/data/therAcid1/bed/
mkdir conservation
cd conservation
cp /cluster/data/metAce1/bed/conservation/HoxD55.q .
cp ../../therAcid1.fa therAcid1.chr
cp /cluster/data/therVolc1/therVolc1.fa therVolc1.chr
cp /cluster/data/picrTorr1/chr.fa picrTorr1.chr
cp /cluster/data/ferrAcid1/chr.fa ferrAcid1.chr
#fix names to be therAcid1, therVolc1, picrTorr1 manually
sed s/\>C/\>ferrAcid1.C/ ferrAcid1.chr | gawk '{if(/ferrAcid1.Contig/){ print $1;}else{print toupper($0);}}' > temp
mv temp ferrAcid1.chr
faToNib therAcid1.chr therAcid1.chr.nib
faToNib therVolc1.chr therVolc1.chr.nib
faToNib picrTorr1.chr picrTorr1.chr.nib
faToTwoBit ferrAcid1.chr ferrAcid1.2bit
#chrom sizes
faSize -detailed *.chr > chrom.sizes
#blastz
blastz therAcid1.chr therVolc1.chr Q=HoxD55.q > therAcid1-therVolc1.lav
blastz therAcid1.chr picrTorr1.chr Q=HoxD55.q > therAcid1-picrTorr1.lav
blastz therAcid1.chr ferrAcid1.chr Q=HoxD55.q > therAcid1-ferrAcid1.lav
/cluster/bin/i386/lavToAxt therAcid1-therVolc1.lav . . therAcid1-therVolc1.axt
/cluster/bin/i386/lavToAxt therAcid1-picrTorr1.lav . . therAcid1-picrTorr1.axt
/cluster/bin/i386/lavToAxt therAcid1-ferrAcid1.lav . ferrAcid1.2bit therAcid1-ferrAcid1.axt
axtBest therAcid1-therVolc1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-therVolc1-best.axt
axtBest therAcid1-picrTorr1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-picrTorr1-best.axt
axtBest therAcid1-ferrAcid1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-ferrAcid1-best.axt
axtToMaf therAcid1-therVolc1-best.axt chrom.sizes chrom.sizes therAcid1-therVolc1.maf
axtToMaf therAcid1-picrTorr1-best.axt chrom.sizes chrom.sizes therAcid1-picrTorr1.maf
axtToMaf therAcid1-ferrAcid1-best.axt chrom.sizes chrom.sizes therAcid1-ferrAcid1.maf
#multiz
#remove extra header lines
multiz therAcid1-therVolc1.maf therAcid1-picrTorr1.maf - > therAcid1-therVolc1-picrTorr1.maf
multiz therAcid1-ferrAcid1.maf therAcid1-therVolc1-picrTorr1.maf - > therAcid1-therVolc1-picrTorr1-ferrAcid1.maf
#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M therAcid1.chr -o SS therAcid1-therVolc1-picrTorr1-ferrAcid1.maf > therAcid1.ss
/cluster/bin/phast/phyloFit -i SS therAcid1.ss -t "(ferrAcid1,(picrTorr1,(therVolc1,therAcid1)))" -o TaTvPtFa
/cluster/bin/phast/msa_view -i SS therAcid1.ss --summary-only
#add GC content to next call
/cluster/bin/phast/phastCons therAcid1.ss TaTvPtFa.mod --gc 0.4133 \
--target-coverage 0.7 --estimate-trees ther-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
/cluster/bin/phast/phastCons therAcid1.ss \
ther-tree.cons.mod,ther-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi therAcid1-elements.bed --score \
--require-informative 0 --seqname chr > cons.dat
wigEncode cons.dat phastCons.wig phastCons.wib
/cluster/bin/phast/draw_tree TaTvPtFa.mod > ther-tree.ps
#make ai and jpg files in Illustrator
cp ther-tree.jpg /usr/local/apache/htdocs/images/therAcid1-tree.jpg
#move data
mkdir wib
mv phastCons.wib wib/phastCons.wib
mv phastCons.wig wib/phastCons.wig
ln -s /cluster/data/therAcid1/bed/conservation/wib/phastCons.wib /gbdb/therAcid1/wib
mkdir /gbdb/therAcid1/pwMaf
mkdir -p otherSpp/therVolc1 otherSpp/picrTorr1 otherSpp/ferrAcid1
mv therAcid1-picrTorr1.maf otherSpp/picrTorr1/chr.maf
mv therAcid1-therVolc1.maf otherSpp/therVolc1/chr.maf
mv therAcid1-ferrAcid1.maf otherSpp/ferrAcid1/chr.maf
ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/picrTorr1 /gbdb/therAcid1/pwMaf/picrTorr1_pwMaf
ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/ferrAcid1 /gbdb/therAcid1/pwMaf/ferrAcid1_pwMaf
ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/therVolc1 /gbdb/therAcid1/pwMaf/therVolc1_pwMaf
mkdir multiz
mv therAcid1-therVolc1-picrTorr1-ferrAcid1.maf multiz/chr.maf
ln -s /cluster/data/therAcid1/bed/conservation/multiz /gbdb/therAcid1/multizTaTvPtFa
#load
hgLoadWiggle therAcid1 phastCons /cluster/data/therAcid1/bed/conservation/wib/phastCons.wig
hgLoadMaf -warn therAcid1 multizTaTvPtFa
hgLoadMaf -warn therAcid1 picrTorr1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/picrTorr1_pwMaf
hgLoadMaf -warn therAcid1 ferrAcid1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/ferrAcid1_pwMaf
hgLoadMaf -warn therAcid1 therVolc1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/therVolc1_pwMaf
hgLoadBed therAcid1 phastConsElements therAcid1-elements.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae/therAcid1
#trackDb.ra entry
# track multizTaTvPtFa
# shortLabel Conservation
# longLabel Thermoplasma/Ferroplasma/Picrophilus 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 therVolc1 picrTorr1 ferrAcid1
cvs add trackDb.ra
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizTaTvPtFa.html
cvs commit -m "Details page for multiz track" multizTaTvPtFa.html
# GENBANK PROTEIN-CODING GENES
ssh hgwdev
mkdir /cluster/data/therAcid1/genbank
cd /cluster/data/therAcid1/genbank
cp /projects/lowelab/db/Bacteria/Thermoplasma_acidophilum/ .
mv NC_003552.gbk therAcid1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > therAcid1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > therAcid1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > therAcid1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome therAcid1.gbk therAcid1-params-bed.txt therAcid1-genbank-cds.bed
gbArchaeGenome therAcid1.gbk therAcid1-params-pep.txt therAcid1-genbank-cds.pep
gbArchaeGenome therAcid1.gbk therAcid1-params-xra.txt therAcid1-genbank-cds.xra
hgLoadBed therAcid1 gbProtCode therAcid1-genbank-cds.bed
hgsql therAcid1 < ~/kent/src/hg/lib/pepPred.sql
hgsql therAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql therAcid1
echo rename table minGeneInfo to gbProtCodeXra | hgsql therAcid1
echo load data local infile \'therAcid1-genbank-cds.pep\' into table gbProtCodePep | hgsql therAcid1
echo load data local infile \'therAcid1-genbank-cds.xra\' into table gbProtCodeXra | hgsql therAcid1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' therAcid1-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 therAcid1-genbank-cds.xra > therAcid1.gp
# GENBANK rRNA GENES
ssh hgdev
cd /cluster/data/therAcid1/genbank
gbArchaeGenome -kind=rRNA therAcid1.gbk therAcid1-params-bed.txt therAcid1-rrnas.bed
echo 'gene product NA' > therAcid1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA therAcid1.gbk therAcid1-params-rrna-xra.txt therAcid1-rrnas-xra.txt
hgLoadBed therAcid1 gbRRNA therAcid1-rrnas.bed
hgsql therAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql therAcid1
echo load data local infile \'therAcid1-rrnas-xra.txt\' into table gbRRNAXra | hgsql therAcid1
# 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/therAcid1/bed/loweTrnaGene
cd /cluster/data/therAcid1/bed/loweTrnaGene
hgLoadBed -tab therAcid1 loweTrnaGene therAcid1-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/therAcid1/bed/loweSnoGene
cd /cluster/data/therAcid1/bed/loweSnoGene
hgLoadBed -tab therAcid1 loweSnoGene therAcid1-snos.bed