# 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 10/2/05) mkdir /cluster/store5/archae/therAcid1 ln -s /cluster/store5/archae/therAcid1 /cluster/data/therAcid1 cd /cluster/data/therAcid1 cp /projects/lowelab/db/Bacteria/Thermoplasma_acidophilum/Ther_acid* . mv Ther_acid.fa therAcid1.fa grep ">" therAcid1.fa # Edit header of therAcid1.fa seqs to '>chr >plasmid_pNRC100 >plasmid_pNRC200' faToTwoBit therAcid1.fa therAcid1.2bit mkdir /gbdb/therAcid1 ln -s /cluster/data/therAcid1/therAcid1.2bit /gbdb/therAcid1/therAcid1.2bit # CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 10/2/05) ssh hgwdev echo 'create database therAcid1' | hgsql '' cd /cluster/data/therAcid1 faSize -detailed therAcid1.fa > chrom.sizes echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" | hgsql therAcid1 echo 'INSERT INTO dbDb (name, description, nibPath, organism, defaultPos, active, orderKey, genome, scientificName, htmlPath, hgNearOk) values ("therAcid1", "Sep 2000", "/gbdb/therAcid1", "Thermoplasma acidophilum", "chr:500000-550000", 1, 284, "Thermoplasma acidophilum","Thermoplasma acidophilum DSM 1728", "/gbdb/therAcid1/html/description.html", 0);' | hgsql hgcentraltest echo 'INSERT INTO defaultDb (genome, name) values ("Thermoplasma acidophilum", "therAcid1");' | hgsql hgcentraltest echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Thermoplasma acidophilum", "archaea",85);' | hgsql hgcentraltest # CREATE CHROMINFO TABLE ssh hgwdev cd /cluster/data/therAcid1 cp ~baertsch/kent/src/hg/lib/chromInfo.sql . hgsql therAcid1 < chromInfo.sql echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql therAcid1 echo "update chromInfo set fileName = '/gbdb/therAcid1/therAcid1.2bit'" | hgsql therAcid1 cd ~/kent/src/hg/makeDb/trackDb # add the trackDb directories mkdir -p archae/therAcid1 cvs add archae/therAcid1 cvs commit archae/therAcid1 make DBS=therAcid1 # GC20BASE (DONE 10/2/05) mkdir -p /cluster/data/therAcid1/bed/gc20Base cd /cluster/data/therAcid1/bed/gc20Base hgGcPercent -wigOut -doGaps -file=stdout -overlap=10 -win=20 therAcid1 /cluster/data/therAcid1/ | wigEncode stdin gc20Base.wig gc20Base.wib cd /cluster/data/therAcid1/bed/gc20Base mkdir /gbdb/therAcid1/wib ln -s `pwd`/gc20Base.wib /gbdb/therAcid1/wib hgLoadWiggle -pathPrefix=/gbdb/therAcid1/wib therAcid1 gc20Base gc20Base.wig # verify index is correct: hgsql therAcid1 -e "show index from gc20Base;" # should see good numbers in Cardinality column # TANDEM REPEAT MASKER (DONE 10/2/05) ssh hgwdev mkdir -p /cluster/data/therAcid1/bed/simpleRepeat cd /cluster/data/therAcid1 trfBig therAcid1.fa /dev/null -bedAt=/cluster/data/therAcid1/bed/simpleRepeat/chr.bed cd /cluster/data/therAcid1/bed/simpleRepeat hgLoadBed therAcid1 simpleRepeat *.bed -sqlTable=/cluster/home/lowe/kent/src/hg/lib/simpleRepeat.sql # TIGR GENES (DONE 10/3/05) # 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 genome 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. mkdir /cluster/data/therAcid1/bed/tigrCmrORFs cp therAcid1-tigr.tab /cluster/data/therAcid1/bed/tigrCmrORFs cd /cluster/data/therAcid1/bed/tigrCmrORFs ~aamp/bin/i386/tigrCmrToBed therAcid1-tigr.tab therAcid1-tigr.bed cat therAcid1-tigr.bed | sed -e 's/chr1/chr/' > temp mv temp therAcid1-tigr.bed hgLoadBed -tab therAcid1 tigrCmrGene therAcid1-tigr.bed -sqlTable=/cluster/home/kpollard/kent/src/hg/lib/tigrCmrGene.sql echo "rename table tigrCmrGene to tigrCmrORFs;" | hgsql therAcid1 # DESCRIPTION PAGE (DONE 10/4/05) # Write ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html mkdir -p /cluster/data/therAcid1/html/ cp ~/kent/src/hg/makeDb/trackDb/archae/therAcid1/description.html /cluster/data/therAcid1/html/description.html mkdir -p /gbdb/therAcid1/html ln -s /cluster/data/therAcid1/html/description.html /gbdb/therAcid1/html/ # MULTIZ with therVolc, picrTorr, and ferrAcid # DONE (10/11/05), kpollard cd /cluster/data/therAcid1/bed/ mkdir conservation cd conservation cp /cluster/data/metAce1/bed/conservation/HoxD55.q . cp ../../therAcid1.fa therAcid1.chr cp /cluster/data/therVolc1/therVolc1.fa therVolc1.chr cp /cluster/data/picrTorr1/chr.fa picrTorr1.chr cp /cluster/data/ferrAcid1/chr.fa ferrAcid1.chr #fix names to be therAcid1, therVolc1, picrTorr1 manually sed s/\>C/\>ferrAcid1.C/ ferrAcid1.chr | gawk '{if(/ferrAcid1.Contig/){ print $1;}else{print toupper($0);}}' > temp mv temp ferrAcid1.chr faToNib therAcid1.chr therAcid1.chr.nib faToNib therVolc1.chr therVolc1.chr.nib faToNib picrTorr1.chr picrTorr1.chr.nib faToTwoBit ferrAcid1.chr ferrAcid1.2bit #chrom sizes faSize -detailed *.chr > chrom.sizes #blastz blastz therAcid1.chr therVolc1.chr Q=HoxD55.q > therAcid1-therVolc1.lav blastz therAcid1.chr picrTorr1.chr Q=HoxD55.q > therAcid1-picrTorr1.lav blastz therAcid1.chr ferrAcid1.chr Q=HoxD55.q > therAcid1-ferrAcid1.lav /cluster/bin/i386/lavToAxt therAcid1-therVolc1.lav . . therAcid1-therVolc1.axt /cluster/bin/i386/lavToAxt therAcid1-picrTorr1.lav . . therAcid1-picrTorr1.axt /cluster/bin/i386/lavToAxt therAcid1-ferrAcid1.lav . ferrAcid1.2bit therAcid1-ferrAcid1.axt axtBest therAcid1-therVolc1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-therVolc1-best.axt axtBest therAcid1-picrTorr1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-picrTorr1-best.axt axtBest therAcid1-ferrAcid1.axt therAcid1.chr -winSize=500 -minScore=5000 therAcid1-ferrAcid1-best.axt axtToMaf therAcid1-therVolc1-best.axt chrom.sizes chrom.sizes therAcid1-therVolc1.maf axtToMaf therAcid1-picrTorr1-best.axt chrom.sizes chrom.sizes therAcid1-picrTorr1.maf axtToMaf therAcid1-ferrAcid1-best.axt chrom.sizes chrom.sizes therAcid1-ferrAcid1.maf #multiz #remove extra header lines multiz therAcid1-therVolc1.maf therAcid1-picrTorr1.maf - > therAcid1-therVolc1-picrTorr1.maf multiz therAcid1-ferrAcid1.maf therAcid1-therVolc1-picrTorr1.maf - > therAcid1-therVolc1-picrTorr1-ferrAcid1.maf #phyloHMM /cluster/bin/phast/msa_view -i MAF -M therAcid1.chr -o SS therAcid1-therVolc1-picrTorr1-ferrAcid1.maf > therAcid1.ss /cluster/bin/phast/phyloFit -i SS therAcid1.ss -t "(ferrAcid1,(picrTorr1,(therVolc1,therAcid1)))" -o TaTvPtFa /cluster/bin/phast/msa_view -i SS therAcid1.ss --summary-only #add GC content to next call /cluster/bin/phast/phastCons therAcid1.ss TaTvPtFa.mod --gc 0.4133 \ --target-coverage 0.7 --estimate-trees ther-tree \ --expected-lengths 25 --no-post-probs --ignore-missing \ --nrates 1,1 /cluster/bin/phast/phastCons therAcid1.ss \ ther-tree.cons.mod,ther-tree.noncons.mod \ --target-coverage 0.7 --expected-lengths 25 \ --viterbi therAcid1-elements.bed --score \ --require-informative 0 --seqname chr > cons.dat wigEncode cons.dat phastCons.wig phastCons.wib /cluster/bin/phast/draw_tree TaTvPtFa.mod > ther-tree.ps #make ai and jpg files in Illustrator cp ther-tree.jpg /usr/local/apache/htdocs/images/therAcid1-tree.jpg #move data mkdir wib mv phastCons.wib wib/phastCons.wib mv phastCons.wig wib/phastCons.wig ln -s /cluster/data/therAcid1/bed/conservation/wib/phastCons.wib /gbdb/therAcid1/wib mkdir /gbdb/therAcid1/pwMaf mkdir -p otherSpp/therVolc1 otherSpp/picrTorr1 otherSpp/ferrAcid1 mv therAcid1-picrTorr1.maf otherSpp/picrTorr1/chr.maf mv therAcid1-therVolc1.maf otherSpp/therVolc1/chr.maf mv therAcid1-ferrAcid1.maf otherSpp/ferrAcid1/chr.maf ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/picrTorr1 /gbdb/therAcid1/pwMaf/picrTorr1_pwMaf ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/ferrAcid1 /gbdb/therAcid1/pwMaf/ferrAcid1_pwMaf ln -s /cluster/data/therAcid1/bed/conservation/otherSpp/therVolc1 /gbdb/therAcid1/pwMaf/therVolc1_pwMaf mkdir multiz mv therAcid1-therVolc1-picrTorr1-ferrAcid1.maf multiz/chr.maf ln -s /cluster/data/therAcid1/bed/conservation/multiz /gbdb/therAcid1/multizTaTvPtFa #load hgLoadWiggle therAcid1 phastCons /cluster/data/therAcid1/bed/conservation/wib/phastCons.wig hgLoadMaf -warn therAcid1 multizTaTvPtFa hgLoadMaf -warn therAcid1 picrTorr1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/picrTorr1_pwMaf hgLoadMaf -warn therAcid1 ferrAcid1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/ferrAcid1_pwMaf hgLoadMaf -warn therAcid1 therVolc1_pwMaf -pathPrefix=/gbdb/therAcid1/pwMaf/therVolc1_pwMaf hgLoadBed therAcid1 phastConsElements therAcid1-elements.bed #trackDb cd ~/kent/src/hg/makeDb/trackDb/archae/therAcid1 #trackDb.ra entry # track multizTaTvPtFa # shortLabel Conservation # longLabel Thermoplasma/Ferroplasma/Picrophilus 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 therVolc1 picrTorr1 ferrAcid1 cvs add trackDb.ra cvs commit -m "New multiz track" trackDb.ra #html page cvs add multizTaTvPtFa.html cvs commit -m "Details page for multiz track" multizTaTvPtFa.html # GENBANK PROTEIN-CODING GENES ssh hgwdev mkdir /cluster/data/therAcid1/genbank cd /cluster/data/therAcid1/genbank cp /projects/lowelab/db/Bacteria/Thermoplasma_acidophilum/ . mv NC_003552.gbk therAcid1.gbk # Create 3 files to assist parsing of the genbank # 1. for a bed file echo 'chr start end gene 1000 strand' > therAcid1-params-bed.txt # 2. for the peptide parts echo 'gene translation' > therAcid1-params-pep.txt # 3. for the other gene information echo 'gene product note' > therAcid1-params-xra.txt # Now extract the genes and information: gbArchaeGenome therAcid1.gbk therAcid1-params-bed.txt therAcid1-genbank-cds.bed gbArchaeGenome therAcid1.gbk therAcid1-params-pep.txt therAcid1-genbank-cds.pep gbArchaeGenome therAcid1.gbk therAcid1-params-xra.txt therAcid1-genbank-cds.xra hgLoadBed therAcid1 gbProtCode therAcid1-genbank-cds.bed hgsql therAcid1 < ~/kent/src/hg/lib/pepPred.sql hgsql therAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql echo rename table pepPred to gbProtCodePep | hgsql therAcid1 echo rename table minGeneInfo to gbProtCodeXra | hgsql therAcid1 echo load data local infile \'therAcid1-genbank-cds.pep\' into table gbProtCodePep | hgsql therAcid1 echo load data local infile \'therAcid1-genbank-cds.xra\' into table gbProtCodeXra | hgsql therAcid1 #genbank to genePred csh tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' therAcid1-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 therAcid1-genbank-cds.xra > therAcid1.gp # GENBANK rRNA GENES ssh hgdev cd /cluster/data/therAcid1/genbank gbArchaeGenome -kind=rRNA therAcid1.gbk therAcid1-params-bed.txt therAcid1-rrnas.bed echo 'gene product NA' > therAcid1-params-rrna-xra.txt gbArchaeGenome -kind=rRNA therAcid1.gbk therAcid1-params-rrna-xra.txt therAcid1-rrnas-xra.txt hgLoadBed therAcid1 gbRRNA therAcid1-rrnas.bed hgsql therAcid1 < ~/kent/src/hg/lib/minGeneInfo.sql echo rename table minGeneInfo to gbRRNAXra | hgsql therAcid1 echo load data local infile \'therAcid1-rrnas-xra.txt\' into table gbRRNAXra | hgsql therAcid1 # 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/therAcid1/bed/loweTrnaGene cd /cluster/data/therAcid1/bed/loweTrnaGene hgLoadBed -tab therAcid1 loweTrnaGene therAcid1-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/therAcid1/bed/loweSnoGene cd /cluster/data/therAcid1/bed/loweSnoGene hgLoadBed -tab therAcid1 loweSnoGene therAcid1-snos.bed