src/hg/makeDb/doc/methTher1.txt 1.3
1.3 2009/11/25 21:48:41 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/methTher1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/methTher1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/methTher1.txt 26 Jul 2006 16:59:56 -0000 1.2
+++ src/hg/makeDb/doc/methTher1.txt 25 Nov 2009 21:48:41 -0000 1.3
@@ -1,288 +1,288 @@
# 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/methTher1
ln -s /cluster/store5/archae/methTher1 /cluster/data/methTher1
cd /cluster/data/methTher1
cp /projects/lowelab/db/Bacteria/Methanobacterium_thermoautotrophicum/Meth_ther.* .
mv Meth_ther.fa methTher1.fa
grep ">" methTher1.fa
# Edit header of methTher1.fa seqs to '>chr " -- no plasmids to worry about
faToTwoBit methTher1.fa methTher1.2bit
mkdir /gbdb/methTher1
ln -s /cluster/data/methTher1/methTher1.2bit /gbdb/methTher1/methTher1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/05)
ssh hgwdev
echo 'create database methTher1' | hgsql ''
cd /cluster/data/methTher1
faSize -detailed methTher1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" | hgsql methTher1
echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("methTher1", "Aug 1997", "/gbdb/methTher1", "Methanothermobacter thermoautotrophicus", "chr:500000-550000", 1, 240, "Methanothermobacter thermoautotrophicus","Methanothermobacter thermoautotrophicus str. Delta H", "/gbdb/methTher1/html/description.html", 0);' | hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Methanothermobacter thermoautotrophicus", "methTher1");' | hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanothermobacter thermoautotrophicus", "archaea",85);' | hgsql hgcentraltest
# CREATE CHROMINFO TABLE (DONE 10/05)
ssh hgwdev
cd /cluster/data/methTher1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql methTher1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql methTher1
echo "update chromInfo set fileName = '/gbdb/methTher1/methTher1.2bit'" | hgsql methTher1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/methTher1
cvs add archae/methTher1
cvs commit archae/methTher1
make DBS=methTher1
# GC20BASE (DONE 10/13/05), kpollard
mkdir -p /cluster/data/methTher1/bed/gc20Base
cd /cluster/data/methTher1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -win=10 -overlap=15 methTher1 /cluster/data/methTher1/ | wigEncode stdin gc20Base.wig gc20Base.wib
cd /cluster/data/methTher1/bed/gc20Base
mkdir /gbdb/methTher1/wib
ln -s `pwd`/gc20Base.wib /gbdb/methTher1/wib
hgLoadWiggle -pathPrefix=/gbdb/methTher1/wib methTher1 gc20Base gc20Base.wig
# verify index is correct:
hgsql methTher1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE 10/13/05), kpollard
ssh hgwdev
mkdir -p /cluster/data/methTher1/bed/simpleRepeat
cd /cluster/data/methTher1
trfBig methTher1.fa /dev/null -bedAt=/cluster/data/methTher1/bed/simpleRepeat/chr.bed
cd /cluster/data/methTher1/bed/simpleRepeat
hgLoadBed methTher1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql
# MULTIZ (DONE 10/13/05), kpollard
cd /cluster/data/methTher1/bed
mkdir conservation
cd conservation
cp /cluster/data/pyrFur2/bed/conservation/HoxD55.q .
cp /cluster/data/methJann1/bed/conservation/methTher1.chr .
cp /cluster/data/methJann1/bed/conservation/metMar1.chr .
cp /cluster/data/methJann1/bed/conservation/methJann1.chr .
cp /cluster/data/methJann1/bed/conservation/methKand1.chr .
cp /cluster/data/methJann1/bed/conservation/methTher1.chr.nib .
cp /cluster/data/methJann1/bed/conservation/metMar1.chr.nib .
cp /cluster/data/methJann1/bed/conservation/methJann1.2bit .
cp /cluster/data/methJann1/bed/conservation/methKand1.chr.nib .
faSize -detailed *.chr > chrom.sizes
#blastz
blastz methTher1.chr metMar1.chr Q=HoxD55.q > methTher1-metMar1.lav
blastz methTher1.chr methJann1.chr Q=HoxD55.q > methTher1-methJann1.lav
blastz methTher1.chr methKand1.chr Q=HoxD55.q > methTher1-methKand1.lav
lavToAxt methTher1-metMar1.lav . . methTher1-metMar1.axt
lavToAxt methTher1-methJann1.lav . methJann1.2bit methTher1-methJann1.axt
lavToAxt methTher1-methKand1.lav . . methTher1-methKand1.axt
axtBest methTher1-metMar1.axt methTher1.chr -winSize=500 -minScore=5000 methTher1-metMar1-best.axt
axtBest methTher1-methJann1.axt methTher1.chr -winSize=500 -minScore=5000 methTher1-methJann1-best.axt
axtBest methTher1-methKand1.axt methTher1.chr -winSize=500 -minScore=5000 methTher1-methKand1-best.axt
axtToMaf methTher1-metMar1-best.axt chrom.sizes chrom.sizes methTher1-metMar1.maf
axtToMaf methTher1-methJann1-best.axt chrom.sizes chrom.sizes methTher1-methJann1.maf
axtToMaf methTher1-methKand1-best.axt chrom.sizes chrom.sizes methTher1-methKand1.maf
#multiz
#delete extra header lines from maf files
multiz methTher1-metMar1.maf methTher1-methJann1.maf - > methTher1-metMar1-methJann1.maf
multiz methTher1-methKand1.maf methTher1-metMar1-methJann1.maf - > methTher1-metMar1-methJann1-methKand1.maf
#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M methTher1.chr -o SS methTher1-metMar1-methJann1-methKand1.maf > methTher1.ss
/cluster/bin/phast/phyloFit -i SS methTher1.ss -t "(methKand1,(methTher1,(metMar1,methJann1)))"
/cluster/bin/phast/msa_view -i SS methTher1.ss --summary-only
#insert GC content into the following command
/cluster/bin/phast/phastCons methTher1.ss phyloFit.mod --gc 0.4634 \
--target-coverage 0.7 --estimate-trees meth-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
/cluster/bin/phast/phastCons methTher1.ss \
meth-tree.cons.mod,meth-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi methTher1-elements.bed --score \
--require-informative 0 --seqname chr > cons.dat
wigEncode cons.dat phastCons.wig phastCons.wib
draw_tree phyloFit.mod > methTher1-tree.ps
#check that tree is similar to tree from metMar1
#move data
mkdir wib
mv phastCons.wib wib/phastCons.wib
mv phastCons.wig wib/phastCons.wig
ln -s /cluster/data/methTher1/bed/conservation/wib/phastCons.wib /gbdb/methTher1/wib
mkdir -p /gbdb/methTher1/pwMaf
mkdir -p otherSpp/metMar1 otherSpp/methJann1 otherSpp/methKand1
mv methTher1-metMar1.maf otherSpp/metMar1/chr.maf
mv methTher1-methJann1.maf otherSpp/methJann1/chr.maf
mv methTher1-methKand1.maf otherSpp/methKand1/chr.maf
ln -s /cluster/data/methTher1/bed/conservation/otherSpp/metMar1 /gbdb/methTher1/pwMaf/metMar1_pwMaf
ln -s /cluster/data/methTher1/bed/conservation/otherSpp/methJann1 /gbdb/methTher1/pwMaf/methJann1_pwMaf
ln -s /cluster/data/methTher1/bed/conservation/otherSpp/methKand1 /gbdb/methTher1/pwMaf/methKand1_pwMaf
mkdir multiz
mv methTher1-metMar1-methJann1-methKand1.maf multiz/chr.maf
ln -s /cluster/data/methTher1/bed/conservation/multiz /gbdb/methTher1/multizMtMmMjMk
#load
hgLoadWiggle methTher1 phastCons /cluster/data/methTher1/bed/conservation/wib/phastCons.wig
hgLoadMaf -warn methTher1 multizMtMmMjMk
hgLoadMaf -warn methTher1 metMar1_pwMaf -pathPrefix=/gbdb/methTher1/pwMaf/metMar1_pwMaf
hgLoadMaf -warn methTher1 methJann1_pwMaf -pathPrefix=/gbdb/methTher1/pwMaf/methJann1_pwMaf
hgLoadMaf -warn methTher1 methKand1_pwMaf -pathPrefix=/gbdb/methTher1/pwMaf/methKand1_pwMaf
hgLoadBed methTher1 phastConsElements methTher1-elements.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae/methTher1
#trackDb.ra entry
# track multizMtMmMjMk
# 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 metMar1 methJann1 methKand1
cvs add trackDb.ra
cvs commit -m "Added multiz track" trackDb.ra
#html page for multizMtMmMjMk
cvs add multizMtMmMjMk.html
cvs commit -m "Details page for multiz track" multizMtMmMjMk.html
# DESCRIPTION PAGE (DONE 10/20/05), kpollard
# Write ~/kent/src/hg/makeDb/trackDb/archae/methTher1/description.html
cd ~/kent/src/hg/makeDb/trackDb/archae/methTher1/
chmod a+r description.html
cvs add description.html
cvs commit -m "description page" description.html
mkdir -p /cluster/data/methTher1/html/
cp ~/kent/src/hg/makeDb/trackDb/archae/methTher1/description.html \
/cluster/data/methTher1/html/description.html
mkdir -p /gbdb/methTher1/html
ln -s /cluster/data/methTher1/html/description.html /gbdb/methTher1/html/
# GENBANK PROTEIN-CODING GENES (TO DO)
ssh hgwdev
mkdir /cluster/data/methTher1/genbank
cd /cluster/data/methTher1/genbank
cp /projects/lowelab/db/Bacteria/Sulfolobus_acidocaldarius_DSM_639/ .
mv NC_003552.gbk methTher1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > methTher1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > methTher1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > methTher1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome methTher1.gbk methTher1-params-bed.txt methTher1-genbank-cds.bed
gbArchaeGenome methTher1.gbk methTher1-params-pep.txt methTher1-genbank-cds.pep
gbArchaeGenome methTher1.gbk methTher1-params-xra.txt methTher1-genbank-cds.xra
hgLoadBed methTher1 gbProtCode methTher1-genbank-cds.bed
hgsql methTher1 < ~/kent/src/hg/lib/pepPred.sql
hgsql methTher1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql methTher1
echo rename table minGeneInfo to gbProtCodeXra | hgsql methTher1
echo load data local infile \'methTher1-genbank-cds.pep\' into table gbProtCodePep | hgsql methTher1
echo load data local infile \'methTher1-genbank-cds.xra\' into table gbProtCodeXra | hgsql methTher1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' methTher1-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 methTher1-genbank-cds.xra > methTher1.gp
# GENBANK rRNA GENES (TO DO)
ssh hgdev
cd /cluster/data/methTher1/genbank
gbArchaeGenome -kind=rRNA methTher1.gbk methTher1-params-bed.txt methTher1-rrnas.bed
echo 'gene product NA' > methTher1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA methTher1.gbk methTher1-params-rrna-xra.txt methTher1-rrnas-xra.txt
hgLoadBed methTher1 gbRRNA methTher1-rrnas.bed
hgsql methTher1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql methTher1
echo load data local infile \'methTher1-rrnas-xra.txt\' into table gbRRNAXra | hgsql methTher1
# 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/methTher1/bed/loweTrnaGene
cd /cluster/data/methTher1/bed/loweTrnaGene
hgLoadBed -tab methTher1 loweTrnaGene methTher1-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/methTher1/bed/loweSnoGene
cd /cluster/data/methTher1/bed/loweSnoGene
hgLoadBed -tab methTher1 loweSnoGene methTher1-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/methTher1/bed/tigrCmrORFs
cp methTher1-tigr.tab /cluster/data/methTher1/bed/tigrCmrORFs
cd /cluster/data/methTher1/bed/tigrCmrORFs
/projects/lowelab/users/aamp/bin/i386/tigrCmrToBed methTher1-tigr.tab methTher1-tigr.bed
hgLoadBed -tab methTher1 tigrCmrORFs methTher1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql