# for emacs: -*- mode: sh; -*- # This file describes building the browser database for the archaeal # species Methanosarcina acetivorans. # DOWNLOAD SEQUENCE FROM GENBANK (DONE) ssh eieio mkdir /cluster/store5/archae/methJann1 ln -s /cluster/store5/archae/methJann1 /cluster/data/methJann1 cd /cluster/data/methJann1 cp /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.fna . mv NC_000909.fna NC_000909.fa mv NC_001732.fna NC_001732.fa mv NC_001733.fna NC_001733.fa # Edit header of *.fa to '> methJann1 >smallextrachr >largeextrachr' cat NC_000909.fa NC_001732.fa NC_001733.fa > methJann1.fa faToTwoBit methJann1.fa methJann1.2bit # CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE) ssh hgwdev echo 'create database methJann1' | hgsql '' cd /cluster/data/methJann1 faSize -detailed methJann1.fa > chrom.sizes echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \ | hgsql methJann1 echo 'INSERT INTO dbDb \ (name, description, nibPath, organism, \ defaultPos, active, orderKey, genome, scientificName, \ htmlPath, hgNearOk) values \ ("methJann1", "August 1996", "/gbdb/methJann1", "Methanocaldococcus jannaschii", \ "chr1:500000-550000", 1, 245, "Methanocaldococcus jannaschii", \ "Methanocaldococcus jannaschii DSM 2661", "/gbdb/methJann1/html/description.html", \ 0);' \ | hgsql hgcentraltest echo 'INSERT INTO defaultDb (genome, name) values ("Methanocaldococcus jannaschii", "methJann1");' \ | hgsql hgcentraltest echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanocaldococcus jannaschii", "archaea",85);' \ | hgsql hgcentraltest # CREATE CHROMINFO TABLE (DONE) ssh hgwdev cd /cluster/data/methJann1 cp ~baertsch/kent/src/hg/lib/chromInfo.sql . edit chromInfo.sql; allow fileName to be null hgsql methJann1 < chromInfo.sql echo "load data local infile 'chrom.sizes' into table chromInfo" | hgsql methJann1 echo "update chromInfo set fileName = '/gbdb/methJann1/methJann1.2bit'" | hgsql methJann1 cd ~/kent/src/hg/makeDb/trackDb # add the trackDb directories mkdir -p archae/methJann1 cvs add archae/methJann1 cvs commit cd ~/kent/src/hg/makeDb/trackDb # edit the trackDb makefile # add the trackDb directories mkdir -p archae/methJann1 cvs add archae cvs add archae/methJann1 cvs commit # GC20BASE (DONE) ssh kkstore02 mkdir -p /cluster/data/methJann1/bed/gc20Base cd /cluster/data/methJann1/bed/gc20Base hgGcPercent -wigOut -doGaps -file=stdout -win=20 methJann1 \ /cluster/data/methJann1/ | wigEncode stdin gc20Base.wig gc20Base.wib ssh hgwdev cd /cluster/data/methJann1/bed/gc20Base mkdir /gbdb/methJann1/wib ln -s `pwd`/gc20Base.wib /gbdb/methJann1/wib hgLoadWiggle -pathPrefix=/gbdb/methJann1/wib methJann1 gc20Base gc20Base.wig # verify index is correct: hgsql methJann1 -e "show index from gc20Base;" # should see good numbers in Cardinality column # TANDEM REPEAT MASKER (DONE) ssh hgwdev mkdir -p /cluster/data/methJann1/bed/simpleRepeat cd /cluster/data/methJann1 trfBig methJann1.fa /dev/null -bedAt=/cluster/data/methJann1/bed/simpleRepeat/chr.bed cd /cluster/data/methJann1/bed/simpleRepeat hgLoadBed methJann1 simpleRepeat *.bed -sqlTable=~kent/src/hg/lib/simpleRepeat.sql # MULTIZ with metMar1, methKand1, methTher1 # DONE (10/12/05), kpollard cd /cluster/data/methJann1/bed/ mkdir conservation cd conservation cp /cluster/data/metAce1/bed/conservation/HoxD55.q . cp ../../methJann1.fa methJann1.chr cp /cluster/data/metMar1/chr.fa metMar1.chr cp /projects/lowelab/db/Bacteria/Methanobacterium_thermoautotrophicum/Meth_ther.fa methTher1.chr cp /cluster/data/methKand1/methKand1.fa methKand1.chr #fix names to be metMar1, methTher1, methKand1 manually sed s/\>c/\>methJann1.c/ methJann1.chr > temp mv temp methJann1.chr faToNib methKand1.chr methKand1.chr.nib faToNib metMar1.chr metMar1.chr.nib faToNib methTher1.chr methTher1.chr.nib faToTwoBit methJann1.chr methJann1.2bit cat methJann1.chr | gawk 'BEGIN{ind=0;}{if($1==">methJann1.chr2"){ind=1;} if(ind==0){print $0;}}' > methJann1.chr1 cat methJann1.chr | gawk 'BEGIN{ind=1;}{if($1==">methJann1.chr2"){ind=0;} if($1==">methJann1.chr3"){ind=1;} if(ind==0){print $0;}}' > methJann1.chr2 cat methJann1.chr | gawk 'BEGIN{ind=1;}{if($1==">methJann1.chr3"){ind=0;} if(ind==0){print $0;}}' > methJann1.chr3 faToNib methJann1.chr1 methJann1.chr1.nib faToNib methJann1.chr2 methJann1.chr2.nib faToNib methJann1.chr3 methJann1.chr3.nib #chrom sizes faSize -detailed *.chr > chrom.sizes #blastz blastz methJann1.chr1 metMar1.chr Q=HoxD55.q > methJann1.c1-metMar1.lav blastz methJann1.chr2 metMar1.chr Q=HoxD55.q > methJann1.c2-metMar1.lav blastz methJann1.chr3 metMar1.chr Q=HoxD55.q > methJann1.c3-metMar1.lav blastz methJann1.chr1 methTher1.chr Q=HoxD55.q > methJann1.c1-methTher1.lav blastz methJann1.chr2 methTher1.chr Q=HoxD55.q > methJann1.c2-methTher1.lav blastz methJann1.chr3 methTher1.chr Q=HoxD55.q > methJann1.c3-methTher1.lav blastz methJann1.chr1 methKand1.chr Q=HoxD55.q > methJann1.c1-methKand1.lav blastz methJann1.chr2 methKand1.chr Q=HoxD55.q > methJann1.c2-methKand1.lav blastz methJann1.chr3 methKand1.chr Q=HoxD55.q > methJann1.c3-methKand1.lav /cluster/bin/i386/lavToAxt methJann1.c1-metMar1.lav . . methJann1.c1-metMar1.axt /cluster/bin/i386/lavToAxt methJann1.c2-metMar1.lav . . methJann1.c2-metMar1.axt /cluster/bin/i386/lavToAxt methJann1.c3-metMar1.lav . . methJann1.c3-metMar1.axt /cluster/bin/i386/lavToAxt methJann1.c1-methTher1.lav . . methJann1.c1-methTher1.axt /cluster/bin/i386/lavToAxt methJann1.c2-methTher1.lav . . methJann1.c2-methTher1.axt /cluster/bin/i386/lavToAxt methJann1.c3-methTher1.lav . . methJann1.c3-methTher1.axt /cluster/bin/i386/lavToAxt methJann1.c1-methKand1.lav . . methJann1.c1-methKand1.axt /cluster/bin/i386/lavToAxt methJann1.c2-methKand1.lav . . methJann1.c2-methKand1.axt /cluster/bin/i386/lavToAxt methJann1.c3-methKand1.lav . . methJann1.c3-methKand1.axt axtBest methJann1.c1-metMar1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-metMar1-best.axt axtBest methJann1.c2-metMar1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-metMar1-best.axt axtBest methJann1.c3-metMar1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-metMar1-best.axt axtBest methJann1.c1-methTher1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-methTher1-best.axt axtBest methJann1.c2-methTher1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-methTher1-best.axt axtBest methJann1.c3-methTher1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-methTher1-best.axt axtBest methJann1.c1-methKand1.axt methJann1.chr1 -winSize=500 -minScore=5000 methJann1.c1-methKand1-best.axt axtBest methJann1.c2-methKand1.axt methJann1.chr2 -winSize=500 -minScore=5000 methJann1.c2-methKand1-best.axt axtBest methJann1.c3-methKand1.axt methJann1.chr3 -winSize=500 -minScore=5000 methJann1.c3-methKand1-best.axt foreach f(*-best.axt) set b=`basename $f -best.axt` axtToMaf $f chrom.sizes chrom.sizes $b.maf end #multiz #remove extra header lines #chr1 multiz methJann1.c1-metMar1.maf methJann1.c1-methTher1.maf - > methJann1.c1-metMar1-methTher1.maf multiz methJann1.c1-methKand1.maf methJann1.c1-metMar1-methTher1.maf - > methJann1.c1-metMar1-methTher1-methKand1.maf #chr2 multiz methJann1.c2-metMar1.maf methJann1.c2-methTher1.maf - > methJann1.c2-metMar1-methTher1.maf multiz methJann1.c2-methKand1.maf methJann1.c2-metMar1-methTher1.maf - > methJann1.c2-metMar1-methTher1-methKand1.maf #nothing on chr3 multiz methJann1.c3-metMar1.maf methJann1.c3-methTher1.maf - > methJann1.c3-metMar1-methTher1.maf multiz methJann1.c3-methKand1.maf methJann1.c3-metMar1-methTher1.maf - > methJann1.c3-metMar1-methTher1-methKand1.maf #phyloHMM /cluster/bin/phast/msa_view -i MAF -M methJann1.chr1 -o SS methJann1.c1-metMar1-methTher1-methKand1.maf > methJann1.c1.ss /cluster/bin/phast/msa_view -i MAF -M methJann1.chr2 -o SS methJann1.c2-metMar1-methTher1-methKand1.maf > methJann1.c2.ss /cluster/bin/phast/phyloFit -i SS methJann1.c1.ss -t "(methKand1,(methTher1,(metMar1,methJann1)))" -o chr1_MjMmMtMk /cluster/bin/phast/phyloFit -i SS methJann1.c2.ss -t "(methKand1,(methTher1,(metMar1,methJann1)))" -o chr2_MjMmMtMk /cluster/bin/phast/draw_tree chr1_MjMmMtMk.mod > methJann1-tree.ps #just use chr1 model for starting model (more data) /cluster/bin/phast/msa_view -i SS methJann1.c1.ss --summary-only /cluster/bin/phast/msa_view -i SS methJann1.c2.ss --summary-only #add GC content to next call /cluster/bin/phast/phastCons methJann1.c1.ss chr1_MjMmMtMk.mod \ --gc 0.3786 --target-coverage 0.7 --estimate-trees chr1-tree \ --expected-lengths 25 --no-post-probs --ignore-missing \ --nrates 1,1 /cluster/bin/phast/phastCons methJann1.c2.ss chr1_MjMmMtMk.mod \ --gc 0.2856 --target-coverage 0.7 --estimate-trees chr2-tree \ --expected-lengths 25 --no-post-probs --ignore-missing \ --nrates 1,1 #average with phyloBoot to get cons.mod and noncons.mod #ls *.cons.mod > cons.txt #phyloBoot --read-mods '*cons.txt' --output-average ave.cons.mod > cons_summary.txt #ls *.noncons.mod > noncons.txt #phyloBoot --read-mods '*noncons.txt' --output-average ave.noncons.mod > noncons_summary.txt #PROBLEM: Can't do this with different numbers of species in each mod # Here there is no methKand1 in chr2 data. #Again, just use chrom1 model /cluster/bin/phast/phastCons methJann1.c1.ss \ chr1-tree.cons.mod,chr1-tree.noncons.mod \ --target-coverage 0.7 --expected-lengths 25 \ --viterbi chr1_methJann1-elements.bed --score \ --require-informative 0 --seqname chr1 > chr1_cons.dat /cluster/bin/phast/phastCons methJann1.c2.ss \ chr1-tree.cons.mod,chr1-tree.noncons.mod \ --target-coverage 0.7 --expected-lengths 25 \ --viterbi chr2_methJann1-elements.bed --score \ --require-informative 0 --seqname chr2 > chr2_cons.dat wigEncode chr1_cons.dat chr1_phastCons.wig chr1_phastCons.wib wigEncode chr2_cons.dat chr2_phastCons.wig chr2_phastCons.wib #combine phastCons elements into 1 bed file cat chr*.bed > phastCons.bed #move data mkdir wib mv chr*_phastCons.wib wib/. mv chr*_phastCons.wig wib/. ln -s /cluster/data/methJann1/bed/conservation/wib/*.wib /gbdb/methJann1/wib mkdir /gbdb/methJann1/pwMaf mkdir -p otherSpp/metMar1 otherSpp/methTher1 otherSpp/methKand1 mv methJann1.c1-methTher1.maf otherSpp/methTher1/chr1.maf mv methJann1.c2-methTher1.maf otherSpp/methTher1/chr2.maf mv methJann1.c1-metMar1.maf otherSpp/metMar1/chr1.maf mv methJann1.c2-metMar1.maf otherSpp/metMar1/chr2.maf mv methJann1.c1-methKand1.maf otherSpp/methKand1/chr1.maf mv methJann1.c2-methKand1.maf otherSpp/methKand1/chr2.maf ln -s /cluster/data/methJann1/bed/conservation/otherSpp/methTher1 /gbdb/methJann1/pwMaf/methTher1_pwMaf ln -s /cluster/data/methJann1/bed/conservation/otherSpp/methKand1 /gbdb/methJann1/pwMaf/methKand1_pwMaf ln -s /cluster/data/methJann1/bed/conservation/otherSpp/metMar1 /gbdb/methJann1/pwMaf/metMar1_pwMaf mkdir multiz mv methJann1.c1-metMar1-methTher1-methKand1.maf multiz/chr1.maf mv methJann1.c2-metMar1-methTher1-methKand1.maf multiz/chr2.maf ln -s /cluster/data/methJann1/bed/conservation/multiz /gbdb/methJann1/multizMjMmMtMk #load hgLoadWiggle methJann1 phastCons /cluster/data/methJann1/bed/conservation/wib/chr*_phastCons.wig hgLoadMaf -warn methJann1 multizMjMmMtMk hgLoadMaf -warn methJann1 methTher1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/methTher1_pwMaf hgLoadMaf -warn methJann1 methKand1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/methKand1_pwMaf hgLoadMaf -warn methJann1 metMar1_pwMaf -pathPrefix=/gbdb/methJann1/pwMaf/metMar1_pwMaf hgLoadBed methJann1 phastConsElements phastCons.bed #trackDb cd ~/kent/src/hg/makeDb/trackDb/archae mkdir methJann1 cvs add methJann1 cd methJann1 #trackDb.ra entry # track multizMjMmMtMk # 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 methTher1 methKand1 cvs add trackDb.ra cvs commit -m "New multiz track" trackDb.ra #html page cvs add multizMjMmMtMk.html cvs commit -m "Details page for multiz track" multizMjMmMtMk.html # DESCRIPTION PAGE () ssh hgwdev # Write ~/kent/src/hg/makeDb/trackDb/archae/methJann1/description.html chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/methJann1/description.html # Check it in. mkdir /gbdb/methJann1/html ln -s /cluster/data/methJann1/html/description.html /gbdb/methJann1/html/ # GENBANK PROTEIN-CODING GENES () ssh hgwdev mkdir /cluster/data/methJann1/genbank cd /cluster/data/methJann1/genbank cp /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.gbk . mv NC_003552.gbk methJann1.gbk sed -e 's/db_xref="GeneID:/db_xref2="/' methJann1.gbk > methJann1.fix.gbk # Create 3 files to assist parsing of the genbank # 1. for a bed file echo 'chr start end gene 1000 strand' > methJann1-params-bed.txt # 2. for the peptide parts echo 'gene translation' > methJann1-params-pep.txt # 3. for the other gene information echo 'locus_tag db_xref2 product note protein_id db_xref EC_number pseudo' > methJann1-params-xra.txt # Now extract the genes and information: gbArchaeGenome methJann1.fix.gbk methJann1-params-bed.txt methJann1-genbank-cds.bed gbArchaeGenome methJann1.fix.gbk methJann1-params-pep.txt methJann1-genbank-cds.pep gbArchaeGenome methJann1.fix.gbk methJann1-params-xra.txt methJann1-genbank-cds.xra hgsql methJann1 < ~/kent/src/hg/lib/pepPred.sql hgsql methJann1 < ~/kent/src/hg/lib/minGeneInfo.sql echo rename table pepPred to gbProtCodePep | hgsql methJann1 echo rename table minGeneInfo to gbProtCodeXra | hgsql methJann1 echo load data local infile \'methJann1-genbank-cds.pep\' into table gbProtCodePep | hgsql methJann1 echo load data local infile \'methJann1-genbank-cds.xra\' into table gbProtCodeXra | hgsql methJann1 #genbank to genePred csh tawk '{print $1,$2,$3,$4,$5,$6,$2,$3,0,1,$3-$2,0}' methJann1-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 2.2 1.13 1.14 1.15 tmp2.gp methJann1-genbank-cds.xra > methJann1.gp ldHgGene methJann1 refSeq methJann1.gp -predTab -genePredExt # GENBANK rRNA GENES () ssh hgdev cd /cluster/data/methJann1/genbank gbArchaeGenome -kind=rRNA methJann1.gbk methJann1-params-bed.txt methJann1-rrnas.bed echo 'gene product NA' > methJann1-params-rrna-xra.txt gbArchaeGenome -kind=rRNA methJann1.gbk methJann1-params-rrna-xra.txt methJann1-rrnas-xra.txt hgLoadBed methJann1 gbRRNA methJann1-rrnas.bed hgsql methJann1 < ~/kent/src/hg/lib/minGeneInfo.sql echo rename table minGeneInfo to gbRRNAXra | hgsql methJann1 echo load data local infile \'methJann1-rrnas-xra.txt\' into table gbRRNAXra | hgsql methJann1 # COG STUFF grep COG /projects/lowelab/db/Bacteria/Methanococcus_jannaschii/NC_00*.ptt | awk 'NR>3{OFS="\t";print $6,$8,$7}' > COG hgsql methJann1 < /cluster/home/baertsch/kent/src/hg/lib/cogs.sql echo "load data local infile 'COG' into table COG" | hgsql methJann1 # load cog codes hgsql methJann1 < /cluster/data/metAce1/genbank/COGXra.sql # 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/methJann1/bed/loweTrnaGene cd /cluster/data/methJann1/bed/loweTrnaGene hgLoadBed -tab methJann1 loweTrnaGene methJann1-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/methJann1/bed/loweSnoGene cd /cluster/data/methJann1/bed/loweSnoGene hgLoadBed -tab methJann1 loweSnoGene methJann1-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/methJann1/bed/tigrCmrORFs cp methJann1-tigr.tab /cluster/data/methJann1/bed/tigrCmrORFs cd /cluster/data/methJann1/bed/tigrCmrORFs /projects/lowelab/users/aamp/bin/i386/tigrCmrToBed methJann1-tigr.tab methJann1-tigr.bed hgLoadBed -tab methJann1 tigrCmrORFs methJann1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql