src/hg/makeDb/doc/methMaze1.txt 1.3
1.3 2009/11/25 21:48:41 hiram
change autoScaleDefault to autoScale
Index: src/hg/makeDb/doc/methMaze1.txt
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/doc/methMaze1.txt,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/makeDb/doc/methMaze1.txt 26 Jul 2006 16:59:56 -0000 1.2
+++ src/hg/makeDb/doc/methMaze1.txt 25 Nov 2009 21:48:41 -0000 1.3
@@ -1,289 +1,289 @@
# for emacs: -*- mode: sh; -*-
# This file describes building the browser database for the archaeal
# species Methanosarcina mazei Go1.
ssh eieio
mkdir /cluster/store5/archae/methMaze1
ln -s /cluster/store5/archae/methMaze1 /cluster/data/methMaze1
cd /cluster/data/methMaze1
cp /projects/lowelab/db/Bacteria/Methanosarcina_mazei/NC_003901.fna .
cp NC_00390l.fna methMaze1.fa
# Edit header of *.fa to '> chr '
faToTwoBit methMaze1.fa methMaze1.2bit
# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE)
ssh hgwdev
echo 'create database methMaze1' | hgsql ''
cd /cluster/data/methMaze1
faSize -detailed methMaze1.fa > chrom.sizes
echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \
| hgsql methMaze1
echo 'INSERT INTO dbDb \
(name, description, nibPath, organism, \
defaultPos, active, orderKey, genome, scientificName, \
htmlPath, hgNearOk) values \
("methMaze1", "July 2002", "/gbdb/methMaze1", "Methanosarcina mazei", \
"chr:500000-550000", 1, 252, "Methanosarcina mazei", \
"Methanosarcina mazei Go1", "/gbdb/methMaze1/html/description.html", \
0);' \
| hgsql hgcentraltest
echo 'INSERT INTO defaultDb (genome, name) values ("Methanosarcina mazei", "methMaze1");' \
| hgsql hgcentraltest
echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanosarcina mazei", "archaea",85);' \
| hgsql hgcentraltest
# CREATE CHROMINFO TABLE
ssh hgwdev
cd /cluster/data/methMaze1
cp ~baertsch/kent/src/hg/lib/chromInfo.sql .
hgsql methMaze1 < chromInfo.sql
echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql methMaze1
echo "update chromInfo set fileName = '/gbdb/methMaze1/methMaze1.2bit'" | hgsql methMaze1
cd ~/kent/src/hg/makeDb/trackDb
# add the trackDb directories
mkdir -p archae/methMaze1
cvs add archae/methMaze1
cvs commit
# GC20BASE (DONE)
ssh kkstore02
mkdir -p /cluster/data/methMaze1/bed/gc20Base
cd /cluster/data/methMaze1/bed/gc20Base
hgGcPercent -wigOut -doGaps -file=stdout -win=20 methMaze1 \
/cluster/data/methMaze1/ | wigEncode stdin gc20Base.wig gc20Base.wib
ssh hgwdev
cd /cluster/data/methMaze1/bed/gc20Base
mkdir /gbdb/methMaze1/wib
ln -s `pwd`/gc20Base.wib /gbdb/methMaze1/wib
hgLoadWiggle -pathPrefix=/gbdb/methMaze1/wib methMaze1 gc20Base gc20Base.wig
# verify index is correct:
hgsql methMaze1 -e "show index from gc20Base;"
# should see good numbers in Cardinality column
# TANDEM REPEAT MASKER (DONE)
ssh hgwdev
mkdir -p /cluster/data/methMaze1/bed/simpleRepeat
cd /cluster/data/methMaze1
trfBig methMaze1.fa /dev/null -bedAt=/cluster/data/methMaze1/bed/simpleRepeat/chr.bed
cd /cluster/data/methMaze1/bed/simpleRepeat
hgLoadBed methMaze1 simpleRepeat *.bed -sqlTable=/cluster/home/baertsch/kent/src/hg/lib/simpleRepeat.sql
# MULTIZ with other methanogens
# DONE (10/9/05), kpollard
cd /cluster/data/methMaze1/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 .
#fix names to be methMaze1, methBark1, methBurt1
faToNib metMaz1.chr methMaze1.chr.nib
faToTwoBit metBak0.chr metBak0.2bit
faToTwoBit metBur0.chr metBur0.2bit
#chrom sizes
faSize -detailed *.chr > chrom.sizes
#blastz
blastz metMaz1.chr metAce1.chr Q=HoxD55.q > metMaz1-metAce1.lav
blastz metMaz1.chr metBak0.chr Q=HoxD55.q > metMaz1-metBak0.lav
blastz metMaz1.chr metBur0.chr Q=HoxD55.q > metMaz1-metBur0.lav
/cluster/bin/i386/lavToAxt metMaz1-metAce1.lav . . metMaz1-metAce1.axt
/cluster/bin/i386/lavToAxt metMaz1-metBak0.lav . metBak0.2bit metMaz1-metBak0.axt
/cluster/bin/i386/lavToAxt metMaz1-metBur0.lav . metBur0.2bit metMaz1-metBur0.axt
axtBest metMaz1-metAce1.axt metMaz1.chr -winSize=500 -minScore=5000 metMaz1-metAce1-best.axt
axtBest metMaz1-metBak0.axt metMaz1.chr -winSize=500 -minScore=5000 metMaz1-metBak0-best.axt
axtBest metMaz1-metBur0.axt metMaz1.chr -winSize=500 -minScore=5000 metMaz1-metBur0-best.axt
axtToMaf metMaz1-metAce1-best.axt chrom.sizes chrom.sizes metMaz1-metAce1.maf
axtToMaf metMaz1-metBak0-best.axt chrom.sizes chrom.sizes metMaz1-metBak0.maf
axtToMaf metMaz1-metBur0-best.axt chrom.sizes chrom.sizes metMaz1-metBur0.maf
#multiz
#remove extra header lines
multiz metMaz1-metAce1.maf metMaz1-metBak0.maf - > metMaz1-metAce1-metBak0.maf
multiz metMaz1-metBur0.maf metMaz1-metAce1-metBak0.maf - > metMaz1-metAce1-metBak0-metBur0.maf
#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M metMaz1.chr -o SS metMaz1-metAce1-metBak0-metBur0.maf > metMaz1.ss
/cluster/bin/phast/phyloFit -i SS metMaz1.ss -t "(metBur0,(metBak0,(metAce1,metMaz1)))" -o Mz1Ma1Mbk0Mbr0
/cluster/bin/phast/msa_view -i SS metMaz1.ss --summary-only
#add GC content to next call
/cluster/bin/phast/phastCons metMaz1.ss Mz1Ma1Mbk0Mbr0.mod --gc 0.4190 \
--target-coverage 0.7 --estimate-trees met-tree \
--expected-lengths 25 --no-post-probs --ignore-missing \
--nrates 1,1
/cluster/bin/phast/phastCons metMaz1.ss \
met-tree.cons.mod,met-tree.noncons.mod \
--target-coverage 0.7 --expected-lengths 25 \
--viterbi metMaz1-elements.bed --score \
--require-informative 0 --seqname chr > cons.dat
wigEncode cons.dat phastCons.wig phastCons.wib
/cluster/bin/phast/draw_tree Mz1Ma1Mbk0Mbr0.mod > met-tree.ps
#compare to metAce1 tree
#move data
mkdir wib
mv phastCons.wib wib/phastCons.wib
mv phastCons.wig wib/phastCons.wig
ln -s /cluster/data/methMaze1/bed/conservation/wib/phastCons.wib /gbdb/methMaze1/wib
mkdir /gbdb/methMaze1/pwMaf
mkdir -p otherMet/metAce1 otherMet/metBak1 otherMet/metBur0
mv metMaz1-metBak0.maf otherMet/metBak0/chr.maf
mv metMaz1-metAce1.maf otherMet/metAce1/chr.maf
mv metMaz1-metBur0.maf otherMet/metBur0/chr.maf
ln -s /cluster/data/methMaze1/bed/conservation/otherMet/metBak0 /gbdb/methMaze1/pwMaf/methBark0_pwMaf
ln -s /cluster/data/methMaze1/bed/conservation/otherMet/metBur0 /gbdb/methMaze1/pwMaf/methBurt0_pwMaf
ln -s /cluster/data/methMaze1/bed/conservation/otherMet/metAce1 /gbdb/methMaze1/pwMaf/metAce1_pwMaf
mkdir multiz
mv metMaz1-metAce1-metBak0-metBur0.maf multiz/chr.maf
ln -s /cluster/data/methMaze1/bed/conservation/multiz /gbdb/methMaze1/multizMz1Ma1Mbk0Mbr0
#load
hgLoadWiggle methMaze1 phastCons /cluster/data/methMaze1/bed/conservation/wib/phastCons.wig
hgLoadMaf -warn methMaze1 multizMz1Ma1Mbk0Mbr0
hgLoadMaf -warn methMaze1 methBark0_pwMaf -pathPrefix=/gbdb/methMaze1/pwMaf/methBark0_pwMaf
hgLoadMaf -warn methMaze1 methBurt0_pwMaf -pathPrefix=/gbdb/methMaze1/pwMaf/methBurt0_pwMaf
hgLoadMaf -warn methMaze1 metAce1_pwMaf -pathPrefix=/gbdb/methMaze1/pwMaf/metAce1_pwMaf
hgLoadBed methMaze1 phastConsElements metMaz1-elements.bed
#trackDb
cd ~/kent/src/hg/makeDb/trackDb/archae/methMaze1
#trackDb.ra entry
# track multizMz1Ma1Mbk0Mbr0
# shortLabel Cons 4way
# longLabel Methosarcina 4-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 metAce1 methBark1 methBurt1
cvs commit -m "New multiz track" trackDb.ra
#html page
cvs add multizMz1Ma1Mbk0Mbr0.html
cvs commit -m "Details page for multiz track" multizMz1Ma1Mbk0Mbr0.html
# DESCRIPTION PAGE ()
ssh hgwdev
# Write ~/kent/src/hg/makeDb/trackDb/archae/methMaze1/description.html
chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/methMaze1/description.html
# Check it in.
mkdir /gbdb/methMaze1/html
ln -s /cluster/data/methMaze1/html/description.html /gbdb/methMaze1/html/
# GENBANK PROTEIN-CODING GENES ()
ssh hgwdev
mkdir /cluster/data/methMaze1/genbank
cd /cluster/data/methMaze1/genbank
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanosarcina_acetivorans/NC_003552.gbk
mv NC_003552.gbk methMaze1.gbk
# Create 3 files to assist parsing of the genbank
# 1. for a bed file
echo 'chr
start
end
gene
1000
strand' > methMaze1-params-bed.txt
# 2. for the peptide parts
echo 'gene
translation' > methMaze1-params-pep.txt
# 3. for the other gene information
echo 'gene
product
note' > methMaze1-params-xra.txt
# Now extract the genes and information:
gbArchaeGenome methMaze1.gbk methMaze1-params-bed.txt methMaze1-genbank-cds.bed
gbArchaeGenome methMaze1.gbk methMaze1-params-pep.txt methMaze1-genbank-cds.pep
gbArchaeGenome methMaze1.gbk methMaze1-params-xra.txt methMaze1-genbank-cds.xra
hgLoadBed methMaze1 gbProtCode methMaze1-genbank-cds.bed
hgsql methMaze1 < ~/kent/src/hg/lib/pepPred.sql
hgsql methMaze1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table pepPred to gbProtCodePep | hgsql methMaze1
echo rename table minGeneInfo to gbProtCodeXra | hgsql methMaze1
echo load data local infile \'methMaze1-genbank-cds.pep\' into table gbProtCodePep | hgsql methMaze1
echo load data local infile \'methMaze1-genbank-cds.xra\' into table gbProtCodeXra | hgsql methMaze1
#genbank to genePred
csh
tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' methMaze1-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 methMaze1-genbank-cds.xra > methMaze1.gp
# GENBANK rRNA GENES ()
ssh hgdev
cd /cluster/data/methMaze1/genbank
gbArchaeGenome -kind=rRNA methMaze1.gbk methMaze1-params-bed.txt methMaze1-rrnas.bed
echo 'gene product NA' > methMaze1-params-rrna-xra.txt
gbArchaeGenome -kind=rRNA methMaze1.gbk methMaze1-params-rrna-xra.txt methMaze1-rrnas-xra.txt
hgLoadBed methMaze1 gbRRNA methMaze1-rrnas.bed
hgsql methMaze1 < ~/kent/src/hg/lib/minGeneInfo.sql
echo rename table minGeneInfo to gbRRNAXra | hgsql methMaze1
echo load data local infile \'methMaze1-rrnas-xra.txt\' into table gbRRNAXra | hgsql methMaze1
# 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/methMaze1/bed/loweTrnaGene
cd /cluster/data/methMaze1/bed/loweTrnaGene
hgLoadBed -tab methMaze1 loweTrnaGene methMaze1-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/methMaze1/bed/loweSnoGene
cd /cluster/data/methMaze1/bed/loweSnoGene
hgLoadBed -tab methMaze1 loweSnoGene methMaze1-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/methMaze1/bed/tigrCmrORFs
cp methMaze1-tigr.tab /cluster/data/methMaze1/bed/tigrCmrORFs
cd /cluster/data/methMaze1/bed/tigrCmrORFs
/projects/lowelab/users/aamp/bin/i386/tigrCmrToBed methMaze1-tigr.tab methMaze1-tigr.bed
hgLoadBed -tab methMaze1 tigrCmrORFs methMaze1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql