idKeys for Ensembl assemblies were calculated in: /hive/data/outside/ensembl/genomes/release-107/idKeys/keys/ and Ensembl rapidRelease in: /hive/data/outside/ensembl/genomes/rapidRelease/idKeys/GCA/123/456/789/GCA_123456789.1.idKeys.txt New assemblies have been built for genbano, refseq and ucsc *AND* now including all virus and bacteria assemblies in both genbank and refseq. Should see a large jump in the size of the resulting table. Working in: mkdir /hive/data/inside/assemblyEquivalence/2022-10-18 cd /hive/data/inside/assemblyEquivalence/2022-10-18 ln -s /cluster/home/hiram/kent/src/hg/makeDb/doc/assemblyEquivalence/exact.sh . mkdir ensembl refseq genbank ucsc rapidRelease ### XXX ### The refseq and genbank key setup takes a very long time ### since it now includes virus and bacteria ########### refseq keys ################## cd refseq find /hive/data/genomes/asmHubs/refseqBuild/GCF \ -maxdepth 4 -mindepth 4 -type d | while read buildDir do asmId=`basename "${buildDir}"` keySig="${buildDir}/idKeys/${asmId}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$asmId.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${asmId}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > refseq.keySignatures.txt # real 115m40.888s ########### genbank keys ################## cd ../genbank find /hive/data/genomes/asmHubs/genbankBuild/GCA \ -maxdepth 4 -mindepth 4 -type d | while read buildDir do asmId=`basename "${buildDir}"` keySig="${buildDir}/idKeys/${asmId}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$asmId.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${asmId}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > genbank.keySignatures.txt ########### UCSC keys ################## cd ../ucsc ls -d /hive/data/genomes/* | while read dbDir do db=`basename "${dbDir}"` keySig="${dbDir}/bed/idKeys/${db}.keySignature.txt" idKeysDir=`dirname "${keySig}"` if [ -s "${keySig}" ]; then idKeys="$idKeysDir/$db.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${db}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > ucsc.keySignatures.txt # real 0m41.590s ########### Ensembl Rapid Release keys ################## cd ../rapidRelease find /hive/data/outside/ensembl/genomes/rapidRelease/idKeys/GCA \ -maxdepth 4 -mindepth 4 -type f | grep keySignature.txt | while read keySig do asmId=`basename "${keySig}" | sed -e 's/.keySignature.txt//;'` idKeys=`echo "${keySig}" | sed -e 's/keySignature/idKeys/;'` if [ -s "${keySig}" ]; then fullCount=`grep -c . $idKeys` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${keySig}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${asmId}" "${fullCount}" "${uniqueCount}" fi done | sort -k1,1 > rapidRelease.keySignatures.txt # real 0m36.132s ########### Ensembl keys ################## cd ../ensembl # does not always work, use the wget instead # rsync -av --stats \ # rsync://ftp.ensembl.org/ensembl/pub/release-107/species_EnsemblVertebrates.txt \ # ./ wget --timestamping \ ftp://ftp.ensembl.org/pub/release-107/species_EnsemblVertebrates.txt # extract the GCx assembly names: awk -F$'\t' '{printf "%s_%s\n", $6,$5}' species_EnsemblVertebrates.txt \ | grep "^G" | sort > ensembl.v107.asmId.txt # compare this to the ones we have on hand here cut -f2 ../genbank/genbank.keySignatures.txt | sort > genbank.asmId.here.txt wc -l ensembl.v107.asmId.txt genbank.asmId.here.txt | sed -e 's/^/# /;' # 301 ensembl.v107.asmId.txt # 1441571 genbank.asmId.here.txt comm -12 ensembl.v107.asmId.txt genbank.asmId.here.txt | wc -l # 294 # will need to catch up the assembly hubs for these missing 8: comm -23 ensembl.v107.asmId.txt genbank.asmId.here.txt GCA_000001215.4_BDGP6.32 GCA_000004035.1_Meug_1.0 GCA_000090745.2_AnoCar2.0v2 GCA_000224145.1_KH GCA_000409795.2_ChlSab1.1 GCA_008746955.1_ASM874695v1 GCA_900186095.1_CHOK1GS_HDv1 # checking the listings, it isn't clear all these are needed, appears to # be outdated versions at Ensembl, and perhaps only two new ones for # GCA_002776525.2_ASM277652v2 - assembly status: replaced GCA_002776525.3_ASM277652v3 # GCA_008746955.1_ASM874695v1 -> GCA_008746955.1_CAU_Wild1.0 # add a new find for this current one for ensVer in 107 105 104 103 101 100 99 do printf "# running version %s\n" "${ensVer}" 1>&2 find -L /hive/data/outside/ensembl/genomes/release-${ensVer}/idKeys -type f \ | grep keySignature.txt | while read K do idKeysDir=`dirname "${K}"` id=`basename "${K}" | sed -e 's/.keySignature.txt//;'` idKeys="$idKeysDir/$id.idKeys.txt" fullCount=`cat $idKeys | wc -l` uniqueCount=`cut -f1 $idKeys | sort -u | wc -l` keySig=`cat "${K}"` printf "%s\t%s\t%d\t%d\n" "${keySig}" "${id}" "${fullCount}" "${uniqueCount}" done | sort -k1,1 > ensembl-${ensVer}.keySignatures.txt done # real 2m19.537s # put them all together: sort -u ensembl-10?.keySignatures.txt \ ensembl-99.keySignatures.txt > ensembl.keySignatures.txt # something is odd with five of these. Their names changed between # versions but the sum stayed the same. Can't have this. # Find them via cut -f1 ensembl.keySignatures.txt | sort | uniq -c | sort -rn | head 2 7850e2d5dabb6134fdc9d7083f1a3a54 2 2f66b2c181e8de7668a9d3657666aa9b 2 2e374245cf85b32eddf186cf50f28f82 2 298de0770996a131c6f90a49ebebebb8 2 0eec31acf1f1120af29d62874cdd9952 2 009e19516d917fa9cdae10de74e8c3de egrep -h "7850e2d5dabb6134fdc9d7083f1a3a54|2f66b2c181e8de7668a9d3657666aa9b|2e374245cf85b32eddf186cf50f28f82|298de0770996a131c6f90a49ebebebb8|0eec31acf1f1120af29d62874cdd9952|009e19516d917fa9cdae10de74e8c3de" *.txt | cut -f2 | sort | uniq -c 5 Anolis_carolinensis.AnoCar2.0 4 Anolis_carolinensis.AnoCar2.0v2 3 Canis_familiaris.CanFam3.1 5 Canis_lupus_familiaris.CanFam3.1 3 Cyprinus_carpio_german_mirror.German_Mirror_carp_1.0 8 Cyprinus_carpio_germanmirror.German_Mirror_carp_1.0 3 Cyprinus_carpio_hebao_red.Hebao_red_carp_1.0 8 Cyprinus_carpio_hebaored.Hebao_red_carp_1.0 4 Drosophila_melanogaster.BDGP6.28 5 Drosophila_melanogaster.BDGP6.32 7 Gallus_gallus.GRCg6a 2 Gallus_gallus_gca000002315v5.GRCg6a # Eliminate the older names: mv ensembl.keySignatures.txt ensembl.keySignatures.txt.0 sort -u ensembl-10?.keySignatures.txt \ ensembl-99.keySignatures.txt \ | egrep -v -w "Anolis_carolinensis.AnoCar2.0|Canis_familiaris.CanFam3.1|Cyprinus_carpio_germanmirror.German_Mirror_carp_1.0|Cyprinus_carpio_hebaored.Hebao_red_carp_1.0|Drosophila_melanogaster.BDGP6.28|Gallus_gallus.GRCg6a" \ > ensembl.keySignatures.txt # now it should be clean cut -f1 ensembl.keySignatures.txt | sort | uniq -c | sort -rn | head # only count of 1 seen ########### Exact matches ################## cd /hive/data/inside/assemblyEquivalence/2022-10-18 ./exact.sh ~/kent/src/hg/makeDb/doc/assemblyEquivalence/exactTableTsv.pl \ | sort > table.2022-10-18.tsv wc -l table.* 317948 table.2022-10-18.tsv 363928 table.2022-02-07.tsv ########### Near matches ################## mkdir /hive/data/inside/assemblyEquivalence/2022-10-18/notExact cd /hive/data/inside/assemblyEquivalence/2022-10-18/notExact sed -e 's/release-99/release-107/;' \ /cluster/home/hiram/kent/src/hg/makeDb/doc/assemblyEquivalence/runOne > runOne chmod +x runOne ### XXX ### this isn't going to work with the big jump in number of ### genbank/refseq assemblies time (~/kent/src/hg/makeDb/doc/assemblyEquivalence/allByAll.sh) > all.log 2>&1 # real 107m11.347s sed -e 's/\tcount A .*//;' results/match.*.txt > notExact.table.2022-10-18.tsv wc -l notExact.tab* 1258 notExact.table.2022-10-18.tsv 1239 notExact.table.2022-01-26.tsv 1738 notExact.table.2022-02-07.tsv ########### Table contents to load ################## sort -u notExact.table.2022-10-18.tsv ../table.2022-10-18.tsv \ > hgFixed.asmEquivalent.tsv ### Compare to existing: hgsql -N -e 'select * from asmEquivalent;' hgFixed | sort \ > existing.2022-10-18.tsv wc -l hgFixed* 319206 hgFixed.asmEquivalent.tsv 365666 hgFixed.asmEquivalent.tsv.2022-02-07 wc -l hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv 319206 hgFixed.asmEquivalent.tsv 2594 existing.2022-10-18.tsv # since we have so many new ones, will have to count identicals sort existing.2022-10-18.tsv hgFixed.asmEquivalent.tsv | uniq -c \ | sort -rn | awk '$1 > 1' | wc -l # 2308 sort existing.2022-10-18.tsv hgFixed.asmEquivalent.tsv | uniq -c \ | sort -rn | awk '$1 > 1' | sed -e 's/^ \+//;' | cut -d' ' -f2- \ | sort > same.as.before wc -l same.as.b* 2290 same.as.before 2308 same.as.before.2022-02-07 # so why are there so many missing that used to be counted ? sort existing.2022-10-18.tsv same.as.before | uniq -c | awk '$1 > 1' | wc -l # 2290 sort existing.2022-10-18.tsv same.as.before | uniq -c | awk '$1 < 2' \ | sed -e 's/^ \+//;' | cut -d' ' -f2- | sort > why.gone.missing wc -l why* 304 why.gone.missing 286 why.gone.missing.2022-02-07 ### measure source authorities: cut -f3 hgFixed.asmEquivalent.tsv | sort | uniq -c | sort -n 708 ensembl 731 ucsc 1360 rapidRelease 336537 refseq 337454 genbank cut -f3 hgFixed.asmEquivalent.tsv | sort | uniq -c | sort -n ### should be the same as destination authorities: 708 ensembl 731 ucsc 1360 rapidRelease 336537 refseq 337454 genbank cut -f3,4 hgFixed.asmEquivalent.tsv | sort | uniq -c | sort -n -u 24 rapidRelease ucsc 81 ensembl rapidRelease 93 ensembl ucsc 208 ensembl refseq 263 rapidRelease refseq 272 refseq ucsc 326 ensembl genbank 342 genbank ucsc 992 genbank rapidRelease 335794 genbank refseq ### previously: cut -f3 existing.2022-10-18.tsv | sort | uniq -c | sort -n 571 ensembl 612 ucsc 182165 refseq 182318 genbank cut -f3,4 existing.2022-10-18.tsv | sort | uniq -c | sort -n -u 91 ensembl ucsc 187 ensembl refseq 237 refseq ucsc 284 genbank ucsc 293 ensembl genbank 181741 genbank refseq ### How about the important ones: egrep "mm10|mm39|hg38|hg19" hgFixed.asmEquivalent.tsv GCA_000001405.14_GRCh37.p13 hg19 genbank ucsc 297 297 298 GCA_000001405.15_GRCh38 tarIhg38 genbank ucsc 454 455 455 GCA_000001405.28_GRCh38.p13 hg38 genbank ucsc 640 640 640 GCA_000001635.8_GRCm38.p6 mm10 genbank ucsc 239 239 239 GCA_000001635.9_GRCm39 mm39 genbank ucsc 61 61 61 GCF_000001405.25_GRCh37.p13 hg19 refseq ucsc 297 297 298 GCF_000001405.26_GRCh38 tarIhg38 refseq ucsc 454 455 455 GCF_000001635.26_GRCm38.p6 mm10 refseq ucsc 239 239 239 GCF_000001635.27_GRCm39 mm39 refseq ucsc 61 61 61 Mus_musculus.GRCm39 mm39 ensembl ucsc 61 61 61 hg19 GCA_000001405.14_GRCh37.p13 ucsc genbank 297 298 297 hg19 GCF_000001405.25_GRCh37.p13 ucsc refseq 297 298 297 hg38 GCA_000001405.28_GRCh38.p13 ucsc genbank 640 640 640 mm10 GCA_000001635.8_GRCm38.p6 ucsc genbank 239 239 239 mm10 GCF_000001635.26_GRCm38.p6 ucsc refseq 239 239 239 mm39 GCA_000001635.9_GRCm39 ucsc genbank 61 61 61 mm39 GCF_000001635.27_GRCm39 ucsc refseq 61 61 61 mm39 Mus_musculus.GRCm39 ucsc ensembl 61 61 61 tarIhg38 GCA_000001405.15_GRCh38 ucsc genbank 454 455 455 tarIhg38 GCF_000001405.26_GRCh38 ucsc refseq 454 455 455 ### There are a lot more this time. wc -l hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv # 676790 hgFixed.asmEquivalent.tsv # 365666 existing.2022-10-18.tsv join hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv | wc -l 382994 ### probably should *not* be losing any from before: join -v 2 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv | wc -l 6 join -t$'\t' -v 2 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv | cut -f1-4 GCA_000233375.4_ICSASG_v2 Salmo_salar.ICSASG_v2 genbank ensembl GCA_000738735.5_ASM73873v5 GCF_000738735.5_ASM73873v5 genbank refseq Gallus_gallus.GRCg6a GCA_000002315.5_GRCg6a ensembl genbank Gallus_gallus.GRCg6a GCF_000002315.5_GRCg6a ensembl refseq Gallus_gallus.GRCg6a galGal6 ensembl ucsc Salmo_salar.ICSASG_v2 GCA_000233375.4_ICSASG_v2 ensembl genbank # Ensembl changed the name of their galGal6: grep galGal6 hgFixed.asmEquivalent.tsv | cut -f1-4 | grep ensembl Gallus_gallus_gca000002315v5.GRCg6a galGal6 ensembl ucsc galGal6 Gallus_gallus_gca000002315v5.GRCg6a ucsc ensembl # and new assembly for Salmo_salar: GCA_905237065.2_Ssal_v3.1 Salmo_salar.Ssal_v3.1 genbank ensembl GCF_905237065.1_Ssal_v3.1 Salmo_salar.Ssal_v3.1 refseq ensembl join -t$'\t' -v 2 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv \ | cut -f3 | sort | uniq -c 4 ensembl 2 genbank join -t$'\t' -v 2 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv | cut -f4 | sort | uniq -c 1 ensembl 2 genbank 2 refseq 1 ucsc # if not 0, investigate. Sometimes a new assembly is now an # exact match to something where it was a near match before to # a previous assembly of that organism. # In this case, it is the different names same idKeys that were eliminated # this time that weren't taken care of before: join -t$'\t' -v 2 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv \ | cut -f1-3 GCA_000233375.4_ICSASG_v2 Salmo_salar.ICSASG_v2 genbank GCA_000738735.5_ASM73873v5 GCF_000738735.5_ASM73873v5 genbank Gallus_gallus.GRCg6a GCA_000002315.5_GRCg6a ensembl Gallus_gallus.GRCg6a GCF_000002315.5_GRCg6a ensembl Gallus_gallus.GRCg6a galGal6 ensembl Salmo_salar.ICSASG_v2 GCA_000233375.4_ICSASG_v2 ensembl ### there should be some new ones join -v 1 hgFixed.asmEquivalent.tsv existing.2022-10-18.tsv | wc -l 306571 # I believe the large number of new ones this time is because I went to the # trouble of running up the nearMiss for genbank vs. refseq where I did not # before because there were so many. ### There should be no duplicate equivalents: cut -f1,2 hgFixed.asmEquivalent.tsv | sort | uniq -c | sort -rn | head 1 zonAlb1 Zonotrichia_albicollis.Zonotrichia_albicollis-1.0.1 1 zonAlb1 GCF_000385455.1_Zonotrichia_albicollis-1.0.1 1 zonAlb1 GCA_000385455.1_Zonotrichia_albicollis-1.0.1 1 zaiEbo1 GCF_000848505.1_ViralProj14703 1 zaiEbo1 GCA_000848505.1_ViralProj14703 ... etc ... # none of them indicate '2' they are all unique #### To load up new table contents: hgLoadSqlTab hgFixed asmEquivalent ~/kent/src/hg/lib/asmEquivalent.sql \ hgFixed.asmEquivalent.tsv hgsql -N -e 'select * from asmEquivalent;' hgFixed \ | sort > updated.2022-10-18.tsv wc -l updated* existing* 676790 updated.2022-10-18.tsv 365666 existing.2022-10-18.tsv # Previously: wc -l ../../2022-01-18/notExact/updated.* ../../2022-01-18/notExact/existing.* 319206 ../../2022-01-18/notExact/updated.2022-01-18.tsv 365666 ../../2022-01-18/notExact/updated.2022-02-07.tsv 2594 ../../2022-01-18/notExact/existing.2022-01-18.tsv wc -l ../../2021-05-11/notExact/updated.* ../../2021-05-11/notExact/existing.* 2594 ../../2021-05-11/notExact/updated.2021-05-11.tsv 2546 ../../2021-05-11/notExact/existing.2021-05-11.tsv