# 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 # 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