# for emacs: -*- mode: sh; -*- # This file describes building the browser database for the archaeal # species Methanosarcina acetivorans. # DOWNLOAD SEQUENCE FROM GENBANK (DONE 9/30/05) ssh hgwdev mkdir /cluster/store5/archae/picrTorr1 ln -s /cluster/store5/archae/picrTorr1 /cluster/data/picrTorr1 cd /cluster/data/picrTorr1 cp /projects/lowelab/db/Bacteria/Picrophilus_torridus_DSM_9790/Picr_torr_DSM_9790.fa chr.fa # Edit header of chr.fa to '> picrTorr1' # CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 9/30/05) echo 'create database picrTorr1' | hgsql '' cd /cluster/data/picrTorr1 mkdir nib faToNib chr.fa nib/chr.nib hgNibSeq picrTorr1 /cluster/data/picrTorr1/nib chr.fa faSize -detailed chr.fa > chrom.sizes mkdir -p /gbdb/picrTorr1/nib echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \ | hgsql picrTorr1 echo 'INSERT INTO dbDb \ (name, description, nibPath, organism, \ defaultPos, active, orderKey, genome, scientificName, \ htmlPath, hgNearOk) values \ ("picrTorr1", "June 2004", "/gbdb/picrTorr1/nib", "Picrophilus torridus", \ "chr:500000-550000", 1, 282, "Picrophilus torridus", \ "Picrophilus torridus DSM", "/gbdb/picrTorr1/html/description.html", \ 0);' \ | hgsql hgcentraltest echo 'INSERT INTO defaultDb (genome, name) values ("Picrophilus torridus", "picrTorr1");' \ | hgsql hgcentraltest echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Picrophilus torridus", "archaea",282);' \ | hgsql hgcentraltest cd ~/kent/src/hg/makeDb/trackDb # add the trackDb directories mkdir -p archae/picrTorr1 cvs add archae/picrTorr1 cvs commit archae/picrTorr1 # GC20BASE (DONE - 9/30/05) mkdir -p /cluster/data/picrTorr1/bed/gc20Base cd /cluster/data/picrTorr1/bed/gc20Base hgGcPercent -wigOut -doGaps -file=stdout -win=20 picrTorr1 \ /cluster/data/picrTorr1/nib | wigEncode stdin gc20Base.wig gc20Base.wib cd /cluster/data/picrTorr1/bed/gc20Base mkdir /gbdb/picrTorr1/wib ln -s `pwd`/gc20Base.wib /gbdb/picrTorr1/wib hgLoadWiggle -pathPrefix=/gbdb/picrTorr1/wib picrTorr1 gc20Base gc20Base.wig # verify index is correct: check cardinality column hgsql picrTorr1 -e "show index from gc20Base;" # TANDEM REPEAT MASKER (DONE - 9/30/05) mkdir -p /cluster/data/picrTorr1/bed/simpleRepeat cd /cluster/data/picrTorr1 trfBig chr.fa /dev/null -bedAt=/cluster/data/picrTorr1/bed/simpleRepeat/chr.bed cd /cluster/data/picrTorr1/bed/simpleRepeat cat chr.bed | sed -e 's/picrTorr1/chr/' > temp mv temp chr.bed hgLoadBed picrTorr1 simpleRepeat *.bed -sqlTable=/cluster/home/kpollard/kent/src/hg/lib/simpleRepeat.sql # TIGR GENES (FINISHED 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/picrTorr1/bed/tigrCmrORFs cp picrTorr1-tigr.tab /cluster/data/picrTorr1/bed/tigrCmrORFs cd /cluster/data/picrTorr1/bed/tigrCmrORFs ~aamp/bin/i386/tigrCmrToBed picrTorr1-tigr.tab picrTorr1-tigr.bed cat picrTorr1-tigr.bed | sed -e 's/chr1/chr/' > temp mv temp picrTorr1-tigr.bed hgLoadBed -tab picrTorr1 tigrCmrGene picrTorr1-tigr.bed -sqlTable=/cluster/home/kpollard/kent/src/hg/lib/tigrCmrGene.sql echo "rename table tigrCmrGene to tigrCmrORFs;" | hgsql picrTorr1 # DESCRIPTION PAGE (DONE 10/3/05) # Write ~/kent/src/hg/makeDb/trackDb/archae/picrTorr1/description.html chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/picrTorr1/description.html # Check it in. mkdir -p /cluster/data/picrTorr1/html/ cp ~/kent/src/hg/makeDb/trackDb/archae/picrTorr1/description.html /cluster/data/picrTorr1/html/description.html mkdir /gbdb/picrTorr1/html ln -s /cluster/data/picrTorr1/html/description.html /gbdb/picrTorr1/html/ # MULTIZ with therVolc, therAcid, and ferrAcid # DONE (10/11/05), kpollard cd /cluster/data/picrTorr1/bed/ mkdir conservation cd conservation cp /cluster/data/therAcid1/bed/conservation/HoxD55.q . cp /cluster/data/therAcid1/bed/conservation/*.chr . cp /cluster/data/therAcid1/bed/conservation/*.nib . cp /cluster/data/therAcid1/bed/conservation/*.2bit . #chrom sizes faSize -detailed *.chr > chrom.sizes #blastz blastz picrTorr1.chr therAcid1.chr Q=HoxD55.q > picrTorr1-therAcid1.lav blastz picrTorr1.chr therVolc1.chr Q=HoxD55.q > picrTorr1-therVolc1.lav blastz picrTorr1.chr ferrAcid1.chr Q=HoxD55.q > picrTorr1-ferrAcid1.lav /cluster/bin/i386/lavToAxt picrTorr1-therAcid1.lav . . picrTorr1-therAcid1.axt /cluster/bin/i386/lavToAxt picrTorr1-therVolc1.lav . . picrTorr1-therVolc1.axt /cluster/bin/i386/lavToAxt picrTorr1-ferrAcid1.lav . ferrAcid1.2bit picrTorr1-ferrAcid1.axt axtBest picrTorr1-therAcid1.axt picrTorr1.chr -winSize=500 -minScore=5000 picrTorr1-therAcid1-best.axt axtBest picrTorr1-therVolc1.axt picrTorr1.chr -winSize=500 -minScore=5000 picrTorr1-therVolc1-best.axt axtBest picrTorr1-ferrAcid1.axt picrTorr1.chr -winSize=500 -minScore=5000 picrTorr1-ferrAcid1-best.axt axtToMaf picrTorr1-therAcid1-best.axt chrom.sizes chrom.sizes picrTorr1-therAcid1.maf axtToMaf picrTorr1-therVolc1-best.axt chrom.sizes chrom.sizes picrTorr1-therVolc1.maf axtToMaf picrTorr1-ferrAcid1-best.axt chrom.sizes chrom.sizes picrTorr1-ferrAcid1.maf #multiz #remove extra header lines multiz picrTorr1-therAcid1.maf picrTorr1-therVolc1.maf - > picrTorr1-therAcid1-therVolc1.maf multiz picrTorr1-ferrAcid1.maf picrTorr1-therAcid1-therVolc1.maf - > picrTorr1-therAcid1-therVolc1-ferrAcid1.maf #phyloHMM /cluster/bin/phast/msa_view -i MAF -M picrTorr1.chr -o SS picrTorr1-therAcid1-therVolc1-ferrAcid1.maf > picrTorr1.ss /cluster/bin/phast/phyloFit -i SS picrTorr1.ss -t "(ferrAcid1,(picrTorr1,(therAcid1,therVolc1)))" -o PtTaTvFa /cluster/bin/phast/msa_view -i SS picrTorr1.ss --summary-only #add GC content to next call /cluster/bin/phast/phastCons picrTorr1.ss PtTaTvFa.mod --gc 0.3966 \ --target-coverage 0.7 --estimate-trees ther-tree \ --expected-lengths 25 --no-post-probs --ignore-missing \ --nrates 1,1 /cluster/bin/phast/phastCons picrTorr1.ss \ ther-tree.cons.mod,ther-tree.noncons.mod \ --target-coverage 0.7 --expected-lengths 25 \ --viterbi picrTorr1-elements.bed --score \ --require-informative 0 --seqname chr > cons.dat wigEncode cons.dat phastCons.wig phastCons.wib /cluster/bin/phast/draw_tree PtTaTvFa.mod > ther-tree.ps #compare to therAcid1 tree. #move data mkdir wib mv phastCons.wib wib/phastCons.wib mv phastCons.wig wib/phastCons.wig ln -s /cluster/data/picrTorr1/bed/conservation/wib/phastCons.wib /gbdb/picrTorr1/wib mkdir /gbdb/picrTorr1/pwMaf mkdir -p otherSpp/therAcid1 otherSpp/therVolc1 otherSpp/ferrAcid1 mv picrTorr1-therVolc1.maf otherSpp/therVolc1/chr.maf mv picrTorr1-therAcid1.maf otherSpp/therAcid1/chr.maf mv picrTorr1-ferrAcid1.maf otherSpp/ferrAcid1/chr.maf ln -s /cluster/data/picrTorr1/bed/conservation/otherSpp/therVolc1 /gbdb/picrTorr1/pwMaf/therVolc1_pwMaf ln -s /cluster/data/picrTorr1/bed/conservation/otherSpp/ferrAcid1 /gbdb/picrTorr1/pwMaf/ferrAcid1_pwMaf ln -s /cluster/data/picrTorr1/bed/conservation/otherSpp/therAcid1 /gbdb/picrTorr1/pwMaf/therAcid1_pwMaf mkdir multiz mv picrTorr1-therAcid1-therVolc1-ferrAcid1.maf multiz/chr.maf ln -s /cluster/data/picrTorr1/bed/conservation/multiz /gbdb/picrTorr1/multizPtTaTvFa #load hgLoadWiggle picrTorr1 phastCons /cluster/data/picrTorr1/bed/conservation/wib/phastCons.wig hgLoadMaf -warn picrTorr1 multizPtTaTvFa hgLoadMaf -warn picrTorr1 therVolc1_pwMaf -pathPrefix=/gbdb/picrTorr1/pwMaf/therVolc1_pwMaf hgLoadMaf -warn picrTorr1 ferrAcid1_pwMaf -pathPrefix=/gbdb/picrTorr1/pwMaf/ferrAcid1_pwMaf hgLoadMaf -warn picrTorr1 therAcid1_pwMaf -pathPrefix=/gbdb/picrTorr1/pwMaf/therAcid1_pwMaf hgLoadBed picrTorr1 phastConsElements picrTorr1-elements.bed #trackDb cd ~/kent/src/hg/makeDb/trackDb/archae/picrTorr1 #trackDb.ra entry # track multizPtTaTvFa # 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 therAcid1 therVolc1 ferrAcid1 cvs add trackDb.ra cvs commit -m "New multiz track" trackDb.ra #html page cvs add multizPtTaTvFa.html cvs commit -m "Details page for multiz track" multizPtTaTvFa.html