src/hg/makeDb/doc/sulfAcid1.txt 1.3
1.3 2009/11/25 21:48:42 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/sulfAcid1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/sulfAcid1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/sulfAcid1.txt 26 Jul 2006 16:59:59 -0000 1.2
+++ src/hg/makeDb/doc/sulfAcid1.txt 25 Nov 2009 21:48:42 -0000 1.3
@@ -1,275 +1,275 @@
# 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 10/05)
mkdir /cluster/store5/archae/sulfAcid1
ln -s /cluster/store5/archae/sulfAcid1 /cluster/data/sulfAcid1
cd /cluster/data/sulfAcid1
cp /projects/lowelab/db/Bacteria/Sulfolobus_acidocaldarius_DSM_639/Sulf_acid* .
mv Sulf_acid_DSM_639.fa sulfAcid1.fa
grep ">" sulfAcid1.fa
# Edit header of sulfAcid1.fa seqs to '>chr >plasmid_pNRC100 >plasmid_pNRC200'
faToTwoBit sulfAcid1.fa sulfAcid1.2bit
mkdir /gbdb/sulfAcid1
ln -s /cluster/data/sulfAcid1/sulfAcid1.2bit /gbdb/sulfAcid1/sulfAcid1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/05)
ssh hgwdev
echo 'create database sulfAcid1' | hgsql ''
cd /cluster/data/sulfAcid1
faSize -detailed sulfAcid1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \
| hgsql sulfAcid1
echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("sulfAcid1", "July 2005", "/gbdb/sulfAcid1", "Sulfolobus acidocaldarius", "chr:500000-550000", 1, 220, "Sulfolobus acidocaldarius","Sulfolobus acidocaldarius DSM 639", "/gbdb/sulfAcid1/html/description.html", 0);' | hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Sulfolobus acidocaldarius", "sulfAcid1");' | hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Sulfolobus acidocaldarius", "archaea",85);' | hgsql hgcentraltest
# CREATE CHROMINFO TABLE (DONE 10/05)
ssh hgwdev
cd /cluster/data/sulfAcid1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql sulfAcid1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql sulfAcid1
echo "update chromInfo set fileName = '/gbdb/sulfAcid1/sulfAcid1.2bit'" | hgsql sulfAcid1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/sulfAcid1
cvs add archae/sulfAcid1
cvs commit archae/sulfAcid1
make DBS=sulfAcid1
# GC20BASE (DONE 10/05)
mkdir -p /cluster/data/sulfAcid1/bed/gc20Base
cd /cluster/data/sulfAcid1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -win=20 sulfAcid1 /cluster/data/sulfAcid1/ | wigEncode stdin gc20Base.wig gc20Base.wib
cd /cluster/data/sulfAcid1/bed/gc20Base
mkdir /gbdb/sulfAcid1/wib
ln -s `pwd`/gc20Base.wib /gbdb/sulfAcid1/wib
hgLoadWiggle -pathPrefix=/gbdb/sulfAcid1/wib sulfAcid1 gc20Base gc20Base.wig
# verify index is correct:
hgsql sulfAcid1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE 10/05)
ssh hgwdev
mkdir -p /cluster/data/sulfAcid1/bed/simpleRepeat
cd /cluster/data/sulfAcid1
trfBig sulfAcid1.fa /dev/null -bedAt=/cluster/data/sulfAcid1/bed/simpleRepeat/chr.bed
cd /cluster/data/sulfAcid1/bed/simpleRepeat
hgLoadBed sulfAcid1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql
# MULTIZ (DONE 10/8/05)
cd /cluster/data/sulfAcid1/bed
mkdir conservation
cd conservation
cp /cluster/data/pyrFur2/bed/conservation/HoxD55.q .
cp /cluster/data/sulSol1/bed/conservation/sulAci1.chr sulfAcid1.chr
cp /cluster/data/sulSol1/bed/conservation/sulTok1.chr sulfToko1.chr
cp /cluster/data/sulSol1/bed/conservation/sulSol1.chr .
#edit headers for Aci and Tok to be sulfAcid1, sulfToko1
/cluster/bin/i386/faToNib sulfAcid1.chr sulfAcid1.chr.nib
/cluster/bin/i386/faToNib sulfToko1.chr sulfToko1.chr.nib
cp /cluster/data/sulSol1/bed/conservation/sulSol1.chr.nib .
faSize -detailed *.chr > chrom.sizes
#blastz for Aci-Tok
blastz sulfAcid1.chr sulfToko1.chr Q=HoxD55.q > sulfAcid1-sulfToko1.lav
/cluster/bin/i386/lavToAxt sulfAcid1-sulfToko1.lav . . sulfAcid1-sulfToko1.axt
axtBest sulfAcid1-sulfToko1.axt sulfAcid1.chr -winSize=500 -minScore=5000 sulfAcid1-sulfToko1-best.axt
axtToMaf sulfAcid1-sulfToko1-best.axt chrom.sizes chrom.sizes sulfAcid1-sulfToko1.maf
#blastz for Aci-Sol
blastz sulfAcid1.chr sulSol1.chr Q=HoxD55.q > sulfAcid1-sulSol1.lav
/cluster/bin/i386/lavToAxt sulfAcid1-sulSol1.lav . . sulfAcid1-sulSol1.axt
axtBest sulfAcid1-sulSol1.axt sulfAcid1.chr -winSize=500 -minScore=5000 sulfAcid1-sulSol1-best.axt
axtToMaf sulfAcid1-sulSol1-best.axt chrom.sizes chrom.sizes sulfAcid1-sulSol1.maf
#multiz
#delete extra header lines from maf files
multiz sulfAcid1-sulfToko1.maf sulfAcid1-sulSol1.maf - > sulfAcid1-sulfToko1-sulSol1.maf
#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M sulfAcid1.chr -o SS sulfAcid1-sulfToko1-sulSol1.maf > sulfAcid1.ss
/cluster/bin/phast/phyloFit -i SS sulfAcid1.ss -t "(sulSol1,(sulfToko1,sulfAcid1))"
/cluster/bin/phast/msa_view -i SS sulfAcid1.ss --summary-only
/cluster/bin/phast/phastCons sulfAcid1.ss phyloFit.mod --gc 0.3507 \
--target-coverage 0.7 --estimate-trees sul-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
/cluster/bin/phast/phastCons sulfAcid1.ss \
sul-tree.cons.mod,sul-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi sulfAcid1-elements.bed --score \
--require-informative 0 --seqname chr > cons.dat
wigEncode cons.dat phastCons.wig phastCons.wib
draw_tree phyloFit.mod > sulfAcid1-tree.ps
#check that tree is similar to sul-tree.ps from sulSol1
#move data
mkdir wib
mv phastCons.wib wib/phastCons.wib
mv phastCons.wig wib/phastCons.wig
ln -s /cluster/data/sulfAcid1/bed/conservation/wib/phastCons.wib /gbdb/sulfAcid1/wib
mkdir -p /gbdb/sulfAcid1/pwMaf
mkdir -p otherSul/sulfToko1 otherSul/sulSol1
mv sulfAcid1-sulfToko1.maf otherSul/sulfToko1/chr.maf
mv sulfAcid1-sulSol1.maf otherSul/sulSol1/chr.maf
ln -s /cluster/data/sulfAcid1/bed/conservation/otherSul/sulfToko1 /gbdb/sulfAcid1/pwMaf/sulfToko1_pwMaf
ln -s /cluster/data/sulfAcid1/bed/conservation/otherSul/sulSol1 /gbdb/sulfAcid1/pwMaf/sulSol1_pwMaf
mkdir multiz
mv sulfAcid1-sulfToko1-sulSol1.maf multiz/chr.maf
ln -s /cluster/data/sulfAcid1/bed/conservation/multiz /gbdb/sulfAcid1/multizSa1St1Ss1
#load
hgLoadWiggle sulfAcid1 phastCons /cluster/data/sulfAcid1/bed/conservation/wib/phastCons.wig
hgLoadMaf -warn sulfAcid1 multizSa1St1Ss1
hgLoadMaf -warn sulfAcid1 sulfToko1_pwMaf -pathPrefix=/gbdb/sulfAcid1/pwMaf/sulfToko1_pwMaf
hgLoadMaf -warn sulfAcid1 sulSol1_pwMaf -pathPrefix=/gbdb/sulfAcid1/pwMaf/sulSol1_pwMaf
hgLoadBed sulfAcid1 phastConsElements sulfAcid1-elements.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae
mkdir sulfAcid1
cvs add sulfAcid1
cd sulfAcid1
#trackDb.ra entry
# track multizSa1St1Ss1
# shortLabel Conservation
# longLabel Sulfolobus 3-way 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 sulfToko1 sulSol1
cvs add trackDb.ra
cvs commit -m "Added multiz track" trackDb.ra
#html page for multizSa1St1Ss1
cd ~/kent/src/hg/makeDb/trackDb/archae/sulfAcid1
cvs add multizSa1St1Ss1.html
cvs commit -m "Details page for multiz track" multizSa1St1Ss1.html
# DESCRIPTION PAGE (DONE 10/20/05), kpollard
# Write ~/kent/src/hg/makeDb/trackDb/archae/sulfAcid1/description.html
cd ~/kent/src/hg/makeDb/trackDb/archae/sulfAcid1/
chmod a+r description.html
cvs add description.html
cvs commit -m "description page" description.html
mkdir -p /cluster/data/sulfAcid1/html/
cp ~/kent/src/hg/makeDb/trackDb/archae/sulfAcid1/description.html \
/cluster/data/sulfAcid1/html/description.html
mkdir -p /gbdb/sulfAcid1/html
ln -s /cluster/data/sulfAcid1/html/description.html /gbdb/sulfAcid1/html/
# GENBANK PROTEIN-CODING GENES (TO DO)
ssh hgwdev
mkdir /cluster/data/sulfAcid1/genbank
cd /cluster/data/sulfAcid1/genbank
cp /projects/lowelab/db/Bacteria/Sulfolobus_acidocaldarius_DSM_639/ .
mv NC_003552.gbk sulfAcid1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > sulfAcid1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > sulfAcid1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > sulfAcid1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome sulfAcid1.gbk sulfAcid1-params-bed.txt sulfAcid1-genbank-cds.bed
gbArchaeGenome sulfAcid1.gbk sulfAcid1-params-pep.txt sulfAcid1-genbank-cds.pep
gbArchaeGenome sulfAcid1.gbk sulfAcid1-params-xra.txt sulfAcid1-genbank-cds.xra
hgLoadBed sulfAcid1 gbProtCode sulfAcid1-genbank-cds.bed
hgsql sulfAcid1 < ~/kent/src/hg/lib/pepPred.sql
hgsql sulfAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql sulfAcid1
echo rename table minGeneInfo to gbProtCodeXra | hgsql sulfAcid1
echo load data local infile \'sulfAcid1-genbank-cds.pep\' into table gbProtCodePep | hgsql sulfAcid1
echo load data local infile \'sulfAcid1-genbank-cds.xra\' into table gbProtCodeXra | hgsql sulfAcid1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' sulfAcid1-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 sulfAcid1-genbank-cds.xra > sulfAcid1.gp
# GENBANK rRNA GENES (TO DO)
ssh hgdev
cd /cluster/data/sulfAcid1/genbank
gbArchaeGenome -kind=rRNA sulfAcid1.gbk sulfAcid1-params-bed.txt sulfAcid1-rrnas.bed
echo 'gene product NA' > sulfAcid1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA sulfAcid1.gbk sulfAcid1-params-rrna-xra.txt sulfAcid1-rrnas-xra.txt
hgLoadBed sulfAcid1 gbRRNA sulfAcid1-rrnas.bed
hgsql sulfAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql sulfAcid1
echo load data local infile \'sulfAcid1-rrnas-xra.txt\' into table gbRRNAXra | hgsql sulfAcid1
# 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 (TO DO)
# 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/sulfAcid1/bed/loweTrnaGene
cd /cluster/data/sulfAcid1/bed/loweTrnaGene
hgLoadBed -tab sulfAcid1 loweTrnaGene sulfAcid1-lowe-trnas.bed -sqlTable=~/kent/src/hg/lib/loweTrnaGene.sql
# TODD LOWE snoRNA GENES (TO DO)
# This is a bed 6 file created by hand.
ssh hgwdev
mkdir /cluster/data/sulfAcid1/bed/loweSnoGene
cd /cluster/data/sulfAcid1/bed/loweSnoGene
hgLoadBed -tab sulfAcid1 loweSnoGene sulfAcid1-snos.bed
# TIGR GENES (TO DO)
# 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 "Pyrobaculum aerophilum IM2", 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.
ssh hgwdev
mkdir /cluster/data/sulfAcid1/bed/tigrCmrORFs
cp sulfAcid1-tigr.tab /cluster/data/sulfAcid1/bed/tigrCmrORFs
cd /cluster/data/sulfAcid1/bed/tigrCmrORFs
/projects/lowelab/users/aamp/bin/i386/tigrCmrToBed sulfAcid1-tigr.tab sulfAcid1-tigr.bed
hgLoadBed -tab sulfAcid1 tigrCmrORFs sulfAcid1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql