src/hg/makeDb/doc/methBark1.txt 1.3
1.3 2009/11/25 21:48:40 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/methBark1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/methBark1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/methBark1.txt 26 Jul 2006 16:59:56 -0000 1.2
+++ src/hg/makeDb/doc/methBark1.txt 25 Nov 2009 21:48:40 -0000 1.3
@@ -1,380 +1,380 @@
# for emacs: -*- mode: sh; -*-
# This file describes building the browser database for the archaeal
# species Methanosarcina barkeri
# DOWNLOAD SEQUENCE FROM GENBANK (DONE)
ssh eieio
mkdir /cluster/store5/archae/methBark1
ln -s /cluster/store5/archae/methBark1 /cluster/data/methBark1
cd /cluster/data/methBark1
cp /projects/lowelab/db/Bacteria/Methanosarcina_barkeri_fusaro/NC_0073*.fna .
mv NC_007355.fna chr.fa
mv NC_007349.fna plasmid1.fa
# Edit header of chr.fa and plasmid1.fa to '> chr and >plasmid1
cat chr.fa plasmid1.fa > methBark1.fa
faToTwoBit methBark1.fa methBark1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE)
ssh hgwdev
echo 'create database methBark1' | hgsql ''
cd /cluster/data/methBark1
faSize -detailed methBark1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \
| hgsql methBark1
echo 'INSERT INTO dbDb \
(name, description, nibPath, organism, \
defaultPos, active, orderKey, genome, scientificName, \
htmlPath, hgNearOk) values \
("methBark1", "June 2002", "/gbdb/methBark1", "Methanosarcina barkeri", \
"chr:500000-550000", 1, 251, "Methanosarcina barkeri", \
"Methanosarcina barkeri fusaro", "/gbdb/methBark1/html/description.html", \
0);' \
| hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Methanosarcina barkeri", "methBark1");' \
| hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanosarcina barkeri", "archaea",85);' \
| hgsql hgcentraltest
# CREATE CHROMINFO TABLE (DONE)
ssh hgwdev
cd /cluster/data/methBark1
edit chromInfo.sql; allow fileName to be null
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql methBark1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql methBark1
echo "update chromInfo set fileName = '/gbdb/methBark1/rheMac1.2bit'" | hgsql methBark1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/methBark1
cvs add archae/methBark1
cvs commit
# GC20BASE (DONE)
ssh kkstore02
mkdir -p /cluster/data/methBark1/bed/gc20Base
cd /cluster/data/methBark1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -win=20 methBark1 \
/cluster/data/methBark1/ | wigEncode stdin gc20Base.wig gc20Base.wib
ssh hgwdev
cd /cluster/data/methBark1/bed/gc20Base
mkdir /gbdb/methBark1/wib
ln -s `pwd`/gc20Base.wib /gbdb/methBark1/wib
hgLoadWiggle -pathPrefix=/gbdb/methBark1/wib methBark1 gc20Base gc20Base.wig
# verify index is correct:
hgsql methBark1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE)
ssh hgwdev
mkdir -p /custer/data/methBark1/bed/simpleRepeat
cd /cluster/data/methBark1
trfBig methBark1.fa /dev/null -bedAt=/cluster/data/methBark1/bed/simpleRepeat/chr.bed
cd /cluster/data/methBark1/bed/simpleRepeat
vi chr.bed and replace methBark1 with chr
hgLoadBed methBark1 simpleRepeat *.bed -sqlTable=/cluster/home/baertsch/kent/src/hg/lib/simpleRepeat.sql
# MULTIZ with other methanogens
# DONE (10/15/05), kpollard
cd /cluster/data/methBark1/bed/
mkdir conservation
cd conservation
cp /cluster/data/metAce1/bed/conservation/HoxD55.q .
cp /cluster/data/metAce1/bed/conservation/*.chr .
cp /cluster/data/metAce1/bed/conservation/*.nib .
cp /cluster/data/metAce1/bed/conservation/*.2bit .
#chrom sizes
faSize -detailed *.chr > chrom.sizes
#blastz
blastz metBak0.chr metAce1.chr Q=HoxD55.q > metBak0-metAce1.lav
blastz metBak0.chr metMaz1.chr Q=HoxD55.q > metBak0-metMaz1.lav
blastz metBak0.chr metBur0.2bit Q=HoxD55.q > metBak0-metBur0.lav
/cluster/bin/i386/lavToAxt metBak0-metAce1.lav metBak0.2bit metAce1.2bit metBak0-metAce1.axt
/cluster/bin/i386/lavToAxt metBak0-metMaz1.lav metBak0.2bit . metBak0-metMaz1.axt
/cluster/bin/i386/lavToAxt metBak0-metBur0.lav metBak0.2bit metBur0.2bit metBak0-metBur0.axt
axtBest metBak0-metAce1.axt metBak0.2bit -winSize=500 -minScore=5000 metBak0-metAce1-best.axt
axtBest metBak0-metMaz1.axt metBak0.2bit -winSize=500 -minScore=5000 metBak0-metMaz1-best.axt
axtBest metBak0-metBur0.axt metBak0.2bit -winSize=500 -minScore=5000 metBak0-metBur0-best.axt
axtToMaf metBak0-metAce1-best.axt chrom.sizes chrom.sizes metBak0-metAce1.maf
axtToMaf metBak0-metMaz1-best.axt chrom.sizes chrom.sizes metBak0-metMaz1.maf
axtToMaf metBak0-metBur0-best.axt chrom.sizes chrom.sizes metBak0-metBur0.maf
#STOP: SEEMS TO ONLY USE THE FIRST contig... Need to do separately!
#TRY AGAIN WITH methBark1 (assembled into 1 chr, 1 plasmid)
cd /cluster/data/methBark1/bed
mv conservation conservation.metBak0
mkdir conservation
cd conservation
cp ../conservation.metBak0/HoxD55.q .
cp ../../methBark1.fa .
sed s/chr/methBark1.chr/ methBark1.fa > temp
sed s/plas/methBark1.plas/ temp > methBark1.fa
cp /cluster/data/methBurt1/methBurt1.fa .
sed s/Contig/methBurt1.Contig/ methBurt1.fa > temp
cat temp | gawk '{if(/Contig/){print $1;}else{print toupper($0);}}' > methBurt1.fa
cp /cluster/data/metAce1/bed/conservation/metAce1.chr .
cp /cluster/data/metAce1/bed/conservation/metMaz1.chr methMaze1.chr
sed s/tMaz/thMaze/ methMaze1.chr > temp
mv temp methMaze1.chr
faToNib metAce1.chr metAce1.chr.nib
faToNib methMaze1.chr methMaze1.chr.nib
faToTwoBit methBurt1.fa methBurt1.2bit
faToTwoBit methBark1.fa methBark1.2bit
#chrom sizes
faSize -detailed *.chr *.fa > chrom.sizes
#split methBark1.fa
faSplit byname methBark1.fa ./
echo "chr" > chroms.txt
echo "plasmid1" >> chroms.txt
#blastz
foreach f (`cat chroms.txt`)
echo $f
blastz methBark1.$f.fa metAce1.chr Q=HoxD55.q > methBark1.${f}-metAce1.lav
blastz methBark1.$f.fa methMaze1.chr Q=HoxD55.q > methBark1.${f}-methMaze1.lav
blastz methBark1.$f.fa methBurt1.fa Q=HoxD55.q > methBark1.${f}-methBurt1.lav
end
foreach f (`cat chroms.txt`)
echo $f
echo "lavToAxt"
lavToAxt methBark1.${f}-metAce1.lav methBark1.2bit . methBark1.${f}-metAce1.axt
lavToAxt methBark1.${f}-methMaze1.lav methBark1.2bit . methBark1.${f}-methMaze1.axt
lavToAxt methBark1.${f}-methBurt1.lav methBark1.2bit methBurt1.2bit methBark1.${f}-methBurt1.axt
echo "axtBest"
axtBest methBark1.${f}-metAce1.axt all -winSize=500 -minScore=5000 methBark1.${f}-metAce1-best.axt
axtBest methBark1.${f}-methMaze1.axt all -winSize=500 -minScore=5000 methBark1.${f}-methMaze1-best.axt
axtBest methBark1.${f}-methBurt1.axt all -winSize=500 -minScore=5000 methBark1.${f}-methBurt1-best.axt
echo "axtToMaf"
axtToMaf methBark1.${f}-metAce1-best.axt chrom.sizes chrom.sizes methBark1.${f}-metAce1.maf
axtToMaf methBark1.${f}-methMaze1-best.axt chrom.sizes chrom.sizes methBark1.${f}-methMaze1.maf
axtToMaf methBark1.${f}-methBurt1-best.axt chrom.sizes chrom.sizes methBark1.${f}-methBurt1.maf
end
#multiz
foreach f(*.maf)
cat $f | gawk 'BEGIN{getline; print $0; getline; getline; getline; getline;}{print $0;}' > temp
mv temp $f
end
foreach f(`cat chroms.txt`)
echo $f
multiz methBark1.${f}-metAce1.maf methBark1.${f}-methMaze1.maf - > methBark1.${f}-metAce1-methMaze1.maf
multiz methBark1.${f}-methBurt1.maf methBark1.${f}-metAce1-methMaze1.maf - > methBark1.${f}-metAce1-methMaze1-methBurt1.maf
end
#phyloHMM
foreach f(`cat chroms.txt`)
echo $f
msa_view -i MAF -M methBark1.$f.fa -o SS methBark1.${f}-metAce1-methMaze1-methBurt1.maf > methBark1.$f.ss
cat methBark1.$f.ss | gawk '{if(/^NAMES/){print "NAMES = methBark1,metAce1,methMaze1,methBurt1";} else{print $0;}}' > temp
mv temp methBark1.$f.ss
phyloFit -i SS methBark1.$f.ss -t "(methBurt1,(methBark1,(metAce1,methMaze1)))" -o ${f}_MbaMaMmMbu
end
#chr has the largest NTUPLES (1072) so use it for starting mod
# it shows GC=0.207678+0.206065=0.413743
#add GC content to next call
foreach f(`cat chroms.txt`)
echo $f
phastCons methBark1.$f.ss chr_MbaMaMmMbu.mod \
--gc 0.4137 --target-coverage 0.7 --estimate-trees ${f} \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
end
foreach f(*.cons.mod)
set b=$f:r:r
echo $b
phastCons methBark1.$b.ss chr.cons.mod,chr.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi ${b}_methBark1-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 *elements.bed > phastCons.bed
#move data
mkdir wib
mv chr_phastCons.wib wib/.
mv plasmid1_phastCons.wib wib/.
mv chr_phastCons.wig wib/.
mv plasmid1_phastCons.wig wib/.
ln -s /cluster/data/methBark1/bed/conservation/wib/*.wib /gbdb/methBark1/wib
mkdir /gbdb/methBark1/pwMaf
mkdir -p otherSpp/metAce1 otherSpp/methMaze1 otherSpp/methBurt1
foreach f(`cat chroms.txt`)
echo $f
mv methBark1.${f}-metAce1.maf otherSpp/metAce1/$f.maf
mv methBark1.${f}-methMaze1.maf otherSpp/methMaze1/$f.maf
mv methBark1.${f}-methBurt1.maf otherSpp/methBurt1/$f.maf
end
ln -s /cluster/data/methBark1/bed/conservation/otherSpp/metAce1 /gbdb/methBark1/pwMaf/metAce1_pwMaf
ln -s /cluster/data/methBark1/bed/conservation/otherSpp/methBurt1 /gbdb/methBark1/pwMaf/methBurt1_pwMaf
ln -s /cluster/data/methBark1/bed/conservation/otherSpp/methMaze1 /gbdb/methBark1/pwMaf/methMaze1_pwMaf
mkdir multiz
foreach f(`cat chroms.txt`)
echo $f
mv methBark1.${f}-metAce1-methMaze1-methBurt1.maf multiz/$f.maf
end
ln -s /cluster/data/methBark1/bed/conservation/multiz /gbdb/methBark1/multizMbaMaMmMbu
#load
hgLoadWiggle methBark1 phastCons /cluster/data/methBark1/bed/conservation/wib/*_phastCons.wig
hgLoadMaf -warn methBark1 multizMbaMaMmMbu
hgLoadMaf -warn methBark1 metAce1_pwMaf -pathPrefix=/gbdb/methBark1/pwMaf/metAce1_pwMaf
hgLoadMaf -warn methBark1 methBurt1_pwMaf -pathPrefix=/gbdb/methBark1/pwMaf/methBurt1_pwMaf
hgLoadMaf -warn methBark1 methMaze1_pwMaf -pathPrefix=/gbdb/methBark1/pwMaf/methMaze1_pwMaf
hgLoadBed methBark1 phastConsElements phastCons.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae/
mkdir methBark1
cvs add methBark1
cd methBark1
#trackDb.ra entry
# track multizMbaMaMmMbu
# 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 metAce1 methMaze1 methBurt1
cvs add trackDb.ra
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizMbaMaMmMbu.html
cvs commit -m "Details page for multiz track" multizMbaMaMmMbu.html
# DESCRIPTION PAGE ()
ssh hgwdev
# Write ~/kent/src/hg/makeDb/trackDb/archae/methBark1/description.html
chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/methBark1/description.html
# Check it in.
mkdir /gbdb/methBark1/html
ln -s /cluster/data/methBark1/html/description.html /gbdb/methBark1/html/
# GENBANK PROTEIN-CODING GENES ()
ssh hgwdev
mkdir /cluster/data/methBark1/genbank
cd /cluster/data/methBark1/genbank
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanosarcina_acetivorans/NC_003552.gbk
mv NC_003552.gbk methBark1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > methBark1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > methBark1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > methBark1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome methBark1.gbk methBark1-params-bed.txt methBark1-genbank-cds.bed
gbArchaeGenome methBark1.gbk methBark1-params-pep.txt methBark1-genbank-cds.pep
gbArchaeGenome methBark1.gbk methBark1-params-xra.txt methBark1-genbank-cds.xra
hgLoadBed methBark1 gbProtCode methBark1-genbank-cds.bed
hgsql methBark1 < ~/kent/src/hg/lib/pepPred.sql
hgsql methBark1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql methBark1
echo rename table minGeneInfo to gbProtCodeXra | hgsql methBark1
echo load data local infile \'methBark1-genbank-cds.pep\' into table gbProtCodePep | hgsql methBark1
echo load data local infile \'methBark1-genbank-cds.xra\' into table gbProtCodeXra | hgsql methBark1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' methBark1-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 methBark1-genbank-cds.xra > methBark1.gp
# GENBANK rRNA GENES ()
ssh hgdev
cd /cluster/data/methBark1/genbank
gbArchaeGenome -kind=rRNA methBark1.gbk methBark1-params-bed.txt methBark1-rrnas.bed
echo 'gene product NA' > methBark1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA methBark1.gbk methBark1-params-rrna-xra.txt methBark1-rrnas-xra.txt
hgLoadBed methBark1 gbRRNA methBark1-rrnas.bed
hgsql methBark1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql methBark1
echo load data local infile \'methBark1-rrnas-xra.txt\' into table gbRRNAXra | hgsql methBark1
# 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/methBark1/bed/loweTrnaGene
cd /cluster/data/methBark1/bed/loweTrnaGene
hgLoadBed -tab methBark1 loweTrnaGene methBark1-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/methBark1/bed/loweSnoGene
cd /cluster/data/methBark1/bed/loweSnoGene
hgLoadBed -tab methBark1 loweSnoGene methBark1-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/methBark1/bed/tigrCmrORFs
cp methBark1-tigr.tab /cluster/data/methBark1/bed/tigrCmrORFs
cd /cluster/data/methBark1/bed/tigrCmrORFs
/projects/lowelab/users/aamp/bin/i386/tigrCmrToBed methBark1-tigr.tab methBark1-tigr.bed
hgLoadBed -tab methBark1 tigrCmrORFs methBark1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql