p13 / p6 for RefSeq

thelovelab · Jan 29, 2024 · 629509e · 629509e
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diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,7 @@
-# tximeta 1.21.2
+# tximeta 1.21.3
 
 * GENCODE 44 (H.s.), M34 (M.m), and Ensembl 111
+* RefSeq p13 for human, p6 for mouse
 
 # tximeta 1.20.0
 

diff --git a/inst/extdata/hashtable.csv b/inst/extdata/hashtable.csv
@@ -263,6 +263,7 @@ Ensembl,Drosophila melanogaster,82,BDGP6,ftp://ftp.ensembl.org/pub/release-82/fa
 Ensembl,Drosophila melanogaster,81,BDGP6,ftp://ftp.ensembl.org/pub/release-81/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz ftp://ftp.ensembl.org/pub/release-81/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz,ftp://ftp.ensembl.org/pub/release-81/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.81.gtf.gz,99639e2f2991df0191dc5a0763dae399d0e7a603667e5807936f62a2844b4282
 Ensembl,Drosophila melanogaster,80,BDGP6,ftp://ftp.ensembl.org/pub/release-80/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz ftp://ftp.ensembl.org/pub/release-80/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz,ftp://ftp.ensembl.org/pub/release-80/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.80.gtf.gz,99639e2f2991df0191dc5a0763dae399d0e7a603667e5807936f62a2844b4282
 Ensembl,Drosophila melanogaster,79,BDGP6,ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz ftp://ftp.ensembl.org/pub/release-79/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz,ftp://ftp.ensembl.org/pub/release-79/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.79.gtf.gz,99639e2f2991df0191dc5a0763dae399d0e7a603667e5807936f62a2844b4282
+RefSeq,Homo sapiens,GRCh38.p13,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gff.gz,f288e2f8a4ad43e8a8a237c774a7d4a986fc22f37f551ff57be4bdb9570d9025
 RefSeq,Homo sapiens,GRCh38.p12,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.38_GRCh38.p12/GCF_000001405.38_GRCh38.p12_genomic.gff.gz,3943415aa9cb00d523bdea68efa73eb3d6207d5fbf42561ec8e3fea0055480ec
 RefSeq,Homo sapiens,GRCh38.p11,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.37_GRCh38.p11/GCF_000001405.37_GRCh38.p11_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.37_GRCh38.p11/GCF_000001405.37_GRCh38.p11_genomic.gff.gz,1a65d80468b2a5348d75c7266d1d9327ef93032eb90f9c51bb65da8582cc9829
 RefSeq,Homo sapiens,GRCh38.p10,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.36_GRCh38.p10/GCF_000001405.36_GRCh38.p10_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.36_GRCh38.p10/GCF_000001405.36_GRCh38.p10_genomic.gff.gz,0eac30f9020a4b114ea54fdc5dec648f5305deb82ee46bd34e48f1a710204b26
@@ -275,6 +276,7 @@ RefSeq,Homo sapiens,GRCh38.p4,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/v
 RefSeq,Homo sapiens,GRCh38.p3,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.29_GRCh38.p3/GCF_000001405.29_GRCh38.p3_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.29_GRCh38.p3/GCF_000001405.29_GRCh38.p3_genomic.gff.gz,0674330a25f111e854005a5d8d32f54766034ba44c9b414f760c76ac57e379f9
 RefSeq,Homo sapiens,GRCh38.p2,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.28_GRCh38.p2/GCF_000001405.28_GRCh38.p2_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.28_GRCh38.p2/GCF_000001405.28_GRCh38.p2_genomic.gff.gz,0674330a25f111e854005a5d8d32f54766034ba44c9b414f760c76ac57e379f9
 RefSeq,Homo sapiens,GRCh38.p1,GRCh38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.27_GRCh38.p1/GCF_000001405.27_GRCh38.p1_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.27_GRCh38.p1/GCF_000001405.27_GRCh38.p1_genomic.gff.gz,fbcf014e31d9033f923f378a0053b6c383781d187575e32329d148cffbc3be0e
+RefSeq,Mus musculus,GRCm38.p6,GRCm38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.gff.gz,d5c8319ad577013741702ef47a22e14eaa2bbad20533e6c2b87abdfcda506140
 RefSeq,Mus musculus,GRCm38.p5,GRCm38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.25_GRCm38.p5/GCF_000001635.25_GRCm38.p5_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.25_GRCm38.p5/GCF_000001635.25_GRCm38.p5_genomic.gff.gz,ba4a46771d67b33ad74d7732c782dc3d356784b42821f7f01afddea692c4b9c5
 RefSeq,Mus musculus,GRCm38.p4,GRCm38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.24_GRCm38.p4/GCF_000001635.24_GRCm38.p4_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.24_GRCm38.p4/GCF_000001635.24_GRCm38.p4_genomic.gff.gz,0ec8d4a26aac1cf35bf99736b7ea4fb4369297d590f15252f04b8d047767f6a7
 RefSeq,Mus musculus,GRCm38.p3,GRCm38,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.23_GRCm38.p3/GCF_000001635.23_GRCm38.p3_rna.fna.gz,ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Mus_musculus/all_assembly_versions/GCF_000001635.23_GRCm38.p3/GCF_000001635.23_GRCm38.p3_genomic.gff.gz,4d5f219fdb2e45883a74627c9417626b1d5655d39f364c38c31b4614687b5680

diff --git a/inst/script/metatximeta.R b/inst/script/metatximeta.R
@@ -122,5 +122,5 @@ hashit("Ensembl", "Mus musculus", i, catNC=TRUE, method=m)
 hashit("Ensembl", "Drosophila melanogaster", i, catNC=TRUE, method=m)
 #
 # RefSeq permalink transcriptomes are rarely updated
-# hashit("RefSeq", "Homo sapiens", paste0("GRCh38.p",i), method=m)
-# hashit("RefSeq", "Mus musculus", paste0("GRCm38.p",i), method=m)
+hashit("RefSeq", "Homo sapiens", paste0("GRCh38.p",i), method=m)
+hashit("RefSeq", "Mus musculus", paste0("GRCm38.p",i), method=m)