1834a2b061d8583ee144f1adf0d0ce3c58166d93 hiram Tue Jan 18 16:02:05 2022 -0800 updated to Ensembl v105 and now including all bacteria, virus, fungi, everything no redmine diff --git src/hg/makeDb/doc/assemblyEquivalence/update.2022-01-18.txt src/hg/makeDb/doc/assemblyEquivalence/update.2022-01-18.txt new file mode 100644 index 0000000..0529366 --- /dev/null +++ src/hg/makeDb/doc/assemblyEquivalence/update.2022-01-18.txt @@ -0,0 +1,391 @@ + +idKeys for Ensembl assemblies were +calculated in: /hive/data/outside/ensembl/genomes/release-105/ + +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/2022-01-18 +cd /hive/data/inside/assemblyEquivalence/2022-01-18 + +mkdir ensembl refseq genbank ucsc + +### 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 + +########### 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 + +cd /hive/data/inside/assemblyEquivalence/2022-01-18 +ln -s /cluster/home/hiram/kent/src/hg/makeDb/doc/assemblyEquivalence/exact.sh . + +########### Ensembl keys ################## +cd ../ensembl + +# does not always work, use the wget instead +# rsync -av --stats \ +# rsync://ftp.ensembl.org/ensembl/pub/release-105/species_EnsemblVertebrates.txt \ +# ./ + +wget --timestamping \ +ftp://ftp.ensembl.org/pub/release-105/species_EnsemblVertebrates.txt + +# extract the GCx assembly names: + +awk -F$'\t' '{printf "%s_%s\n", $6,$5}' species_EnsemblVertebrates.txt \ + | grep "^G" | sort > ensembl.v105.asmId.txt + +# compare this to the ones we have on hand here + +cut -f2 ../genbank/genbank.keySignatures.txt | sort > genbank.asmId.here.txt + +wc -l ensembl.v105.asmId.txt genbank.asmId.here.txt | sed -e 's/^/# /;' +# 297 ensembl.v105.asmId.txt +# 533554 genbank.asmId.here.txt + +comm -12 ensembl.v105.asmId.txt genbank.asmId.here.txt | wc -l +# 289 + +# will need to catch up the assembly hubs for these missing 8: +comm -23 ensembl.v105.asmId.txt genbank.asmId.here.txt +# GCA_000001215.4_BDGP6.32 +# GCA_000004035.1_Meug_1.0 +# GCA_000090745.2_AnoCar2.0v2 +# GCA_000224145.1_KH +# GCA_000409795.2_ChlSab1.1 +# GCA_002776525.2_ASM277652v2 +# GCA_008746955.1_ASM874695v1 +# GCA_900186095.1_CHOK1GS_HDv1 + +# checking the listings, it isn't clear all these are needed, appears to +# be outdated versions at Ensembl, and perhaps only two new ones for +# GCA_002776525.2_ASM277652v2 - assembly status: replaced GCA_002776525.3_ASM277652v3 +# GCA_008746955.1_ASM874695v1 -> GCA_008746955.1_CAU_Wild1.0 + +# add a new find for this current one + +find -L /hive/data/outside/ensembl/genomes/release-105/idKeys -type f \ + | grep keySignature.txt | while read K +do + idKeysDir=`dirname "${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-105.keySignatures.txt + +find -L /hive/data/outside/ensembl/genomes/release-104/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-104.keySignatures.txt + +find -L /hive/data/outside/ensembl/genomes/release-103/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-103.keySignatures.txt + +find -L /hive/data/outside/ensembl/genomes/release-101/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-101.keySignatures.txt + +find /hive/data/outside/ensembl/genomes/release-100/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-100.keySignatures.txt + +find /hive/data/outside/ensembl/genomes/release-99/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-99.keySignatures.txt + +# 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 2f66b2c181e8de7668a9d3657666aa9b + 2 2e374245cf85b32eddf186cf50f28f82 + 2 298de0770996a131c6f90a49ebebebb8 + 2 0eec31acf1f1120af29d62874cdd9952 + 2 009e19516d917fa9cdae10de74e8c3de + +egrep -h "2f66b2c181e8de7668a9d3657666aa9b|2e374245cf85b32eddf186cf50f28f82|298de0770996a131c6f90a49ebebebb8|0eec31acf1f1120af29d62874cdd9952|009e19516d917fa9cdae10de74e8c3de" *.txt | cut -f2 | sort | uniq -c + 5 Anolis_carolinensis.AnoCar2.0 + 3 Anolis_carolinensis.AnoCar2.0v2 + 2 Canis_familiaris.CanFam3.1 + 5 Canis_lupus_familiaris.CanFam3.1 + 2 Cyprinus_carpio_german_mirror.German_Mirror_carp_1.0 + 7 Cyprinus_carpio_germanmirror.German_Mirror_carp_1.0 + 2 Cyprinus_carpio_hebao_red.Hebao_red_carp_1.0 + 7 Cyprinus_carpio_hebaored.Hebao_red_carp_1.0 + 4 Drosophila_melanogaster.BDGP6.28 + 4 Drosophila_melanogaster.BDGP6.32 + + # Eliminate the older names: +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" \ + > ensembl.keySignatures.txt + +########### Exact matches ################## + +cd /hive/data/inside/assemblyEquivalence/2022-01-18 +./exact.sh + +~/kent/src/hg/makeDb/doc/assemblyEquivalence/exactTableTsv.pl \ + | sort > table.2022-01-18.tsv + +########### Near matches ################## + +mkdir /hive/data/inside/assemblyEquivalence/2022-01-18/notExact +cd /hive/data/inside/assemblyEquivalence/2022-01-18/notExact + +sed -e 's/release-99/release-105/;' \ + /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 17m52.128s + +sed -e 's/\tcount A .*//;' results/match.*.txt > notExact.table.2022-01-18.tsv +wc -l notExact.table.2022-01-18.tsv +# 1258 notExact.table.2022-01-18.tsv + +########### Table contents to load ################## + +sort -u notExact.table.2022-01-18.tsv ../table.2022-01-18.tsv \ + > hgFixed.asmEquivalent.tsv + +### Compare to existing: +hgsql -N -e 'select * from asmEquivalent;' hgFixed | sort \ + > existing.2022-01-18.tsv + +wc -l hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv + 319206 hgFixed.asmEquivalent.tsv + 2594 existing.2022-01-18.tsv + +# since we have so many new ones, will have to count identicals +sort existing.2022-01-18.tsv hgFixed.asmEquivalent.tsv | uniq -c \ + | sort -rn | awk '$1 > 1' | wc -l +# 2290 + +sort existing.2022-01-18.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.before +# 2290 + +# so why are there so many missing that used to be counted ? + +sort existing.2022-01-18.tsv same.as.before | uniq -c | awk '$1 > 1' | wc -l +# 2290 + +sort existing.2022-01-18.tsv same.as.before | uniq -c | awk '$1 < 2' \ + | sed -e 's/^ \+//;' | cut -d' ' -f2- | sort > why.gone.missing + +wc -l why.gone.missing +# 304 why.gone.missing + + + +### How about the important ones: + +egrep "mm10|mm39|hg38|hg19" hgFixed.asmEquivalent.tsv + +GCA_000001405.28_GRCh38.p13 hg38 genbank ucsc 640 640 640 +GCA_000001635.8_GRCm38.p6 mm10 genbank ucsc 239 239 239 +GCA_000001635.9_GRCm39 mm39 genbank ucsc 61 61 61 +GCF_000001405.39_GRCh38.p13 hg38 refseq ucsc 639 639 640 +GCF_000001635.26_GRCm38.p6 mm10 refseq ucsc 239 239 239 +GCF_000001635.27_GRCm39 mm39 refseq ucsc 61 61 61 +Mus_musculus.GRCm39 mm39 ensembl ucsc 61 61 61 +hg38 GCA_000001405.28_GRCh38.p13 ucsc genbank 640 640 640 +hg38 GCF_000001405.39_GRCh38.p13 ucsc refseq 639 640 639 +mm10 GCA_000001635.8_GRCm38.p6 ucsc genbank 239 239 239 +mm10 GCF_000001635.26_GRCm38.p6 ucsc refseq 239 239 239 +mm39 GCA_000001635.9_GRCm39 ucsc genbank 61 61 61 +mm39 GCF_000001635.27_GRCm39 ucsc refseq 61 61 61 +mm39 Mus_musculus.GRCm39 ucsc ensembl 61 61 61 + +### most should be identical to before +join hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv | wc -l + 5057 + +### probably should *not* be losing any from before: +join -v 2 hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv | wc -l + 134 + +join -v 2 hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv \ + | cut -d' ' -f3 | sort | uniq -c + 6 ensembl + 76 genbank + 41 refseq + 11 ucsc + +join -v 2 hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv | cut -d' ' -f4 | sort | uniq -c + 30 ensembl + 35 genbank + 49 refseq + 20 ucsc + +Examined a couple (canFam3, xenTro9) appeared to have moved to a more exact +match from genbank to refseq. +# if not 0, investigate. Sometimes a new assembly is now an +# exact match to something where it was a near match before to +# a previous assembly of that organism. +# In this case, it is the different names same idKeys that were eliminated +# this time that weren't taken care of before: + + join -t$'\t' -v 2 hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv \ + | cut -f1-3 +Anolis_carolinensis.AnoCar2.0 GCA_000090745.2_AnoCar2.0 ensembl +Anolis_carolinensis.AnoCar2.0 GCF_000090745.1_AnoCar2.0 ensembl +Anolis_carolinensis.AnoCar2.0 anoCar2 ensembl +Canis_familiaris.CanFam3.1 GCF_000002285.3_CanFam3.1 ensembl +Canis_familiaris.CanFam3.1 canFam3 ensembl +Drosophila_melanogaster.BDGP6.28 GCF_000001215.4_Release_6_plus_ISO1_MT ensembl +Drosophila_melanogaster.BDGP6.28 dm6 ensembl + +### note previous comments: +### ### Showing 5 this time: +### ### This is because the nearMiss calculation is only taking place on the +### ### most recent Ensembl release, not all the past ones. These two assemblies +### ### have new version in ens105 release, thus these older Ensembl assemblies +### ### are not being checked for near miss. For now, going to leave these +### ### missing from the table. Can't maintain all older Ensembl equivalents. + +### Esox_lucius.Eluc_V3 GCA_000721915.3_Eluc_V3 ensembl genbank 1018 1019 1018 +### GCA_000721915.3_Eluc_V3 Esox_lucius.Eluc_V3 genbank ensembl 1018 1018 1019 +### Sarcophilus_harrisii.DEVIL7.0 GCA_000189315.1_Devil_ref_v7.0 ensembl genbank 35974 35975 35974 +### Sarcophilus_harrisii.DEVIL7.0 GCF_000189315.1_Devil_ref_v7.0 ensembl refseq 35974 35975 35974 +### Sarcophilus_harrisii.DEVIL7.0 sarHar1 ensembl ucsc 35974 35975 35974 + +### there should be some new ones +join -v 1 hgFixed.asmEquivalent.tsv existing.2022-01-18.tsv | wc -l + 316820 + +### 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 xipMac1 GCA_000241075.1_Xiphophorus_maculatus-4.4.2 + 1 xenTro9 Xenopus_tropicalis.Xenopus_tropicalis_v9.1 +... etc ... + +#### 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.2022-01-18.tsv + +wc -l updated.2022-01-18.tsv existing.2022-01-18.tsv + 319206 updated.2022-01-18.tsv + 2594 existing.2022-01-18.tsv + +# Previously: + 2594 updated.2022-01-18.tsv + 2546 existing.2022-01-18.tsv + + 2546 updated.2021-03-10.tsv + 2344 existing.2021-03-10.tsv