src/hg/makeDb/doc/methJann1.txt 1.3
1.3 2009/11/25 21:48:41 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/methJann1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/methJann1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/methJann1.txt 26 Jul 2006 16:59:56 -0000 1.2
+++ src/hg/makeDb/doc/methJann1.txt 25 Nov 2009 21:48:41 -0000 1.3
@@ -1,377 +1,377 @@
# for emacs: -*- mode: sh; -*-
# This file describes building the browser database for the archaeal
# species Methanosarcina acetivorans.
# DOWNLOAD SEQUENCE FROM GENBANK (DONE)
ssh eieio
mkdir /cluster/store5/archae/methJann1
ln -s /cluster/store5/archae/methJann1 /cluster/data/methJann1
cd /cluster/data/methJann1
cp /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.fna .
mv NC_000909.fna NC_000909.fa
mv NC_001732.fna NC_001732.fa
mv NC_001733.fna NC_001733.fa
# Edit header of *.fa to '> methJann1 >smallextrachr >largeextrachr'
cat NC_000909.fa NC_001732.fa NC_001733.fa > methJann1.fa
faToTwoBit methJann1.fa methJann1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE)
ssh hgwdev
echo 'create database methJann1' | hgsql ''
cd /cluster/data/methJann1
faSize -detailed methJann1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \
| hgsql methJann1
echo 'INSERT INTO dbDb \
(name, description, nibPath, organism, \
defaultPos, active, orderKey, genome, scientificName, \
htmlPath, hgNearOk) values \
("methJann1", "August 1996", "/gbdb/methJann1", "Methanocaldococcus jannaschii", \
"chr1:500000-550000", 1, 245, "Methanocaldococcus jannaschii", \
"Methanocaldococcus jannaschii DSM 2661", "/gbdb/methJann1/html/description.html", \
0);' \
| hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Methanocaldococcus jannaschii", "methJann1");' \
| hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanocaldococcus jannaschii", "archaea",85);' \
| hgsql hgcentraltest
# CREATE CHROMINFO TABLE (DONE)
ssh hgwdev
cd /cluster/data/methJann1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
edit chromInfo.sql; allow fileName to be null
hgsql methJann1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql methJann1
echo "update chromInfo set fileName = '/gbdb/methJann1/methJann1.2bit'" | hgsql methJann1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/methJann1
cvs add archae/methJann1
cvs commit
cd ~/kent/src/hg/makeDb/trackDb
# edit the trackDb makefile
# add the trackDb directories
mkdir -p archae/methJann1
cvs add archae
cvs add archae/methJann1
cvs commit
# GC20BASE (DONE)
ssh kkstore02
mkdir -p /cluster/data/methJann1/bed/gc20Base
cd /cluster/data/methJann1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -win=20 methJann1 \
/cluster/data/methJann1/ | wigEncode stdin gc20Base.wig gc20Base.wib
ssh hgwdev
cd /cluster/data/methJann1/bed/gc20Base
mkdir /gbdb/methJann1/wib
ln -s `pwd`/gc20Base.wib /gbdb/methJann1/wib
hgLoadWiggle -pathPrefix=/gbdb/methJann1/wib methJann1 gc20Base gc20Base.wig
# verify index is correct:
hgsql methJann1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE)
ssh hgwdev
mkdir -p /cluster/data/methJann1/bed/simpleRepeat
cd /cluster/data/methJann1
trfBig methJann1.fa /dev/null -bedAt=/cluster/data/methJann1/bed/simpleRepeat/chr.bed
cd /cluster/data/methJann1/bed/simpleRepeat
hgLoadBed methJann1 simpleRepeat *.bed -sqlTable=~kent/src/hg/lib/simpleRepeat.sql
# MULTIZ with metMar1, methKand1, methTher1
# DONE (10/12/05), kpollard
cd /cluster/data/methJann1/bed/
mkdir conservation
cd conservation
cp /cluster/data/metAce1/bed/conservation/HoxD55.q .
cp ../../methJann1.fa methJann1.chr
cp /cluster/data/metMar1/chr.fa metMar1.chr
cp /projects/lowelab/db/Bacteria/Methanobacterium_thermoautotrophicum/Meth_ther.fa methTher1.chr
cp /cluster/data/methKand1/methKand1.fa methKand1.chr
#fix names to be metMar1, methTher1, methKand1 manually
sed s/\>c/\>methJann1.c/ methJann1.chr > temp
mv temp methJann1.chr
faToNib methKand1.chr methKand1.chr.nib
faToNib metMar1.chr metMar1.chr.nib
faToNib methTher1.chr methTher1.chr.nib
faToTwoBit methJann1.chr methJann1.2bit
cat methJann1.chr | gawk 'BEGIN{ind=0;}{if($1==">methJann1.chr2"){ind=1;} if(ind==0){print $0;}}' > methJann1.chr1
cat methJann1.chr | gawk 'BEGIN{ind=1;}{if($1==">methJann1.chr2"){ind=0;} if($1==">methJann1.chr3"){ind=1;} if(ind==0){print $0;}}' > methJann1.chr2
cat methJann1.chr | gawk 'BEGIN{ind=1;}{if($1==">methJann1.chr3"){ind=0;} if(ind==0){print $0;}}' > methJann1.chr3
faToNib methJann1.chr1 methJann1.chr1.nib
faToNib methJann1.chr2 methJann1.chr2.nib
faToNib methJann1.chr3 methJann1.chr3.nib
#chrom sizes
faSize -detailed *.chr > chrom.sizes
#blastz
blastz methJann1.chr1 metMar1.chr Q=HoxD55.q > methJann1.c1-metMar1.lav
blastz methJann1.chr2 metMar1.chr Q=HoxD55.q > methJann1.c2-metMar1.lav
blastz methJann1.chr3 metMar1.chr Q=HoxD55.q > methJann1.c3-metMar1.lav
blastz methJann1.chr1 methTher1.chr Q=HoxD55.q > methJann1.c1-methTher1.lav
blastz methJann1.chr2 methTher1.chr Q=HoxD55.q > methJann1.c2-methTher1.lav
blastz methJann1.chr3 methTher1.chr Q=HoxD55.q > methJann1.c3-methTher1.lav
blastz methJann1.chr1 methKand1.chr Q=HoxD55.q > methJann1.c1-methKand1.lav
blastz methJann1.chr2 methKand1.chr Q=HoxD55.q > methJann1.c2-methKand1.lav
blastz methJann1.chr3 methKand1.chr Q=HoxD55.q > methJann1.c3-methKand1.lav
/cluster/bin/i386/lavToAxt methJann1.c1-metMar1.lav . . methJann1.c1-metMar1.axt
/cluster/bin/i386/lavToAxt methJann1.c2-metMar1.lav . . methJann1.c2-metMar1.axt
/cluster/bin/i386/lavToAxt methJann1.c3-metMar1.lav . . methJann1.c3-metMar1.axt
/cluster/bin/i386/lavToAxt methJann1.c1-methTher1.lav . . methJann1.c1-methTher1.axt
/cluster/bin/i386/lavToAxt methJann1.c2-methTher1.lav . . methJann1.c2-methTher1.axt
/cluster/bin/i386/lavToAxt methJann1.c3-methTher1.lav . . methJann1.c3-methTher1.axt
/cluster/bin/i386/lavToAxt methJann1.c1-methKand1.lav . . methJann1.c1-methKand1.axt
/cluster/bin/i386/lavToAxt methJann1.c2-methKand1.lav . . methJann1.c2-methKand1.axt
/cluster/bin/i386/lavToAxt methJann1.c3-methKand1.lav . . methJann1.c3-methKand1.axt
axtBest methJann1.c1-metMar1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-metMar1-best.axt
axtBest methJann1.c2-metMar1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-metMar1-best.axt
axtBest methJann1.c3-metMar1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-metMar1-best.axt
axtBest methJann1.c1-methTher1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-methTher1-best.axt
axtBest methJann1.c2-methTher1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-methTher1-best.axt
axtBest methJann1.c3-methTher1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-methTher1-best.axt
axtBest methJann1.c1-methKand1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-methKand1-best.axt
axtBest methJann1.c2-methKand1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-methKand1-best.axt
axtBest methJann1.c3-methKand1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-methKand1-best.axt
foreach f(*-best.axt)
set b=`basename $f -best.axt`
axtToMaf $f chrom.sizes chrom.sizes $b.maf
end
#multiz
#remove extra header lines
#chr1
multiz methJann1.c1-metMar1.maf methJann1.c1-methTher1.maf - > methJann1.c1-metMar1-methTher1.maf
multiz methJann1.c1-methKand1.maf methJann1.c1-metMar1-methTher1.maf - > methJann1.c1-metMar1-methTher1-methKand1.maf
#chr2
multiz methJann1.c2-metMar1.maf methJann1.c2-methTher1.maf - > methJann1.c2-metMar1-methTher1.maf
multiz methJann1.c2-methKand1.maf methJann1.c2-metMar1-methTher1.maf - > methJann1.c2-metMar1-methTher1-methKand1.maf
#nothing on chr3
multiz methJann1.c3-metMar1.maf methJann1.c3-methTher1.maf - > methJann1.c3-metMar1-methTher1.maf
multiz methJann1.c3-methKand1.maf methJann1.c3-metMar1-methTher1.maf - > methJann1.c3-metMar1-methTher1-methKand1.maf
#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M methJann1.chr1 -o SS methJann1.c1-metMar1-methTher1-methKand1.maf > methJann1.c1.ss
/cluster/bin/phast/msa_view -i MAF -M methJann1.chr2 -o SS methJann1.c2-metMar1-methTher1-methKand1.maf > methJann1.c2.ss
/cluster/bin/phast/phyloFit -i SS methJann1.c1.ss -t "(methKand1,(methTher1,(metMar1,methJann1)))" -o chr1_MjMmMtMk
/cluster/bin/phast/phyloFit -i SS methJann1.c2.ss -t "(methKand1,(methTher1,(metMar1,methJann1)))" -o chr2_MjMmMtMk
/cluster/bin/phast/draw_tree chr1_MjMmMtMk.mod > methJann1-tree.ps
#just use chr1 model for starting model (more data)
/cluster/bin/phast/msa_view -i SS methJann1.c1.ss --summary-only
/cluster/bin/phast/msa_view -i SS methJann1.c2.ss --summary-only
#add GC content to next call
/cluster/bin/phast/phastCons methJann1.c1.ss chr1_MjMmMtMk.mod \
--gc 0.3786 --target-coverage 0.7 --estimate-trees chr1-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
/cluster/bin/phast/phastCons methJann1.c2.ss chr1_MjMmMtMk.mod \
--gc 0.2856 --target-coverage 0.7 --estimate-trees chr2-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
#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
# Here there is no methKand1 in chr2 data.
#Again, just use chrom1 model
/cluster/bin/phast/phastCons methJann1.c1.ss \
chr1-tree.cons.mod,chr1-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi chr1_methJann1-elements.bed --score \
--require-informative 0 --seqname chr1 > chr1_cons.dat
/cluster/bin/phast/phastCons methJann1.c2.ss \
chr1-tree.cons.mod,chr1-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi chr2_methJann1-elements.bed --score \
--require-informative 0 --seqname chr2 > chr2_cons.dat
wigEncode chr1_cons.dat chr1_phastCons.wig chr1_phastCons.wib
wigEncode chr2_cons.dat chr2_phastCons.wig chr2_phastCons.wib
#combine phastCons elements into 1 bed file
cat chr*.bed > phastCons.bed
#move data
mkdir wib
mv chr*_phastCons.wib wib/.
mv chr*_phastCons.wig wib/.
ln -s /cluster/data/methJann1/bed/conservation/wib/*.wib /gbdb/methJann1/wib
mkdir /gbdb/methJann1/pwMaf
mkdir -p otherSpp/metMar1 otherSpp/methTher1 otherSpp/methKand1
mv methJann1.c1-methTher1.maf otherSpp/methTher1/chr1.maf
mv methJann1.c2-methTher1.maf otherSpp/methTher1/chr2.maf
mv methJann1.c1-metMar1.maf otherSpp/metMar1/chr1.maf
mv methJann1.c2-metMar1.maf otherSpp/metMar1/chr2.maf
mv methJann1.c1-methKand1.maf otherSpp/methKand1/chr1.maf
mv methJann1.c2-methKand1.maf otherSpp/methKand1/chr2.maf
ln -s /cluster/data/methJann1/bed/conservation/otherSpp/methTher1 /gbdb/methJann1/pwMaf/methTher1_pwMaf
ln -s /cluster/data/methJann1/bed/conservation/otherSpp/methKand1 /gbdb/methJann1/pwMaf/methKand1_pwMaf
ln -s /cluster/data/methJann1/bed/conservation/otherSpp/metMar1 /gbdb/methJann1/pwMaf/metMar1_pwMaf
mkdir multiz
mv methJann1.c1-metMar1-methTher1-methKand1.maf multiz/chr1.maf
mv methJann1.c2-metMar1-methTher1-methKand1.maf multiz/chr2.maf
ln -s /cluster/data/methJann1/bed/conservation/multiz /gbdb/methJann1/multizMjMmMtMk
#load
hgLoadWiggle methJann1 phastCons /cluster/data/methJann1/bed/conservation/wib/chr*_phastCons.wig
hgLoadMaf -warn methJann1 multizMjMmMtMk
hgLoadMaf -warn methJann1 methTher1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/methTher1_pwMaf
hgLoadMaf -warn methJann1 methKand1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/methKand1_pwMaf
hgLoadMaf -warn methJann1 metMar1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/metMar1_pwMaf
hgLoadBed methJann1 phastConsElements phastCons.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae
mkdir methJann1
cvs add methJann1
cd methJann1
#trackDb.ra entry
# track multizMjMmMtMk
# 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 methTher1 methKand1
cvs add trackDb.ra
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizMjMmMtMk.html
cvs commit -m "Details page for multiz track" multizMjMmMtMk.html
# DESCRIPTION PAGE ()
ssh hgwdev
# Write ~/kent/src/hg/makeDb/trackDb/archae/methJann1/description.html
chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/methJann1/description.html
# Check it in.
mkdir /gbdb/methJann1/html
ln -s /cluster/data/methJann1/html/description.html /gbdb/methJann1/html/
# GENBANK PROTEIN-CODING GENES ()
ssh hgwdev
mkdir /cluster/data/methJann1/genbank
cd /cluster/data/methJann1/genbank
cp /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.gbk .
mv NC_003552.gbk methJann1.gbk
sed -e 's/db_xref="GeneID:/db_xref2="/' methJann1.gbk > methJann1.fix.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > methJann1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > methJann1-params-pep.txt
# 3. for the other gene information
echo 'locus_tag
db_xref2
product
note
protein_id
db_xref
EC_number
pseudo' > methJann1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome methJann1.fix.gbk methJann1-params-bed.txt methJann1-genbank-cds.bed
gbArchaeGenome methJann1.fix.gbk methJann1-params-pep.txt methJann1-genbank-cds.pep
gbArchaeGenome methJann1.fix.gbk methJann1-params-xra.txt methJann1-genbank-cds.xra
hgsql methJann1 < ~/kent/src/hg/lib/pepPred.sql
hgsql methJann1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql methJann1
echo rename table minGeneInfo to gbProtCodeXra | hgsql methJann1
echo load data local infile \'methJann1-genbank-cds.pep\' into table gbProtCodePep | hgsql methJann1
echo load data local infile \'methJann1-genbank-cds.xra\' into table gbProtCodeXra | hgsql methJann1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' methJann1-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 2.2 1.13 1.14 1.15 tmp2.gp methJann1-genbank-cds.xra > methJann1.gp
ldHgGene methJann1 refSeq methJann1.gp -predTab -genePredExt
# GENBANK rRNA GENES ()
ssh hgdev
cd /cluster/data/methJann1/genbank
gbArchaeGenome -kind=rRNA methJann1.gbk methJann1-params-bed.txt methJann1-rrnas.bed
echo 'gene product NA' > methJann1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA methJann1.gbk methJann1-params-rrna-xra.txt methJann1-rrnas-xra.txt
hgLoadBed methJann1 gbRRNA methJann1-rrnas.bed
hgsql methJann1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql methJann1
echo load data local infile \'methJann1-rrnas-xra.txt\' into table gbRRNAXra | hgsql methJann1
# COG STUFF
grep COG /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.ptt | awk 'NR>3{OFS="\t";print $6,$8,$7}' > COG
hgsql methJann1 < /cluster/home/baertsch/kent/src/hg/lib/cogs.sql
echo "load data local infile 'COG' into table COG" | hgsql methJann1
# load cog codes
hgsql methJann1 < /cluster/data/metAce1/genbank/COGXra.sql
# 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/methJann1/bed/loweTrnaGene
cd /cluster/data/methJann1/bed/loweTrnaGene
hgLoadBed -tab methJann1 loweTrnaGene methJann1-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/methJann1/bed/loweSnoGene
cd /cluster/data/methJann1/bed/loweSnoGene
hgLoadBed -tab methJann1 loweSnoGene methJann1-snos.bed
# TIGR GENES ()
# 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/methJann1/bed/tigrCmrORFs
cp methJann1-tigr.tab /cluster/data/methJann1/bed/tigrCmrORFs
cd /cluster/data/methJann1/bed/tigrCmrORFs
/projects/lowelab/users/aamp/bin/i386/tigrCmrToBed methJann1-tigr.tab methJann1-tigr.bed
hgLoadBed -tab methJann1 tigrCmrORFs methJann1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql