[med-svn] [Git][med-team/snpeff][upstream] New upstream version 5.1+d+dfsg
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Thu Jun 2 20:41:59 BST 2022
Pierre Gruet pushed to branch upstream at Debian Med / snpeff
Commits:
3a21e7f8 by Pierre Gruet at 2022-06-02T17:24:37+02:00
New upstream version 5.1+d+dfsg
- - - - -
28 changed files:
- README_release.md
- config/snpEff.ENSEMBL_105.config
- config/snpEff.ENSEMBL_BFMPP_52.config
- + config/snpEff.FLYBASE_FB2022_02.config
- config/snpEff.config
- config/snpEff.dbs.config
- docs/examples/index.html
- docs/index.html
- docs/sitemap.xml.gz
- docs/versions.txt
- galaxy/tool-data/snpEff_genomes.loc
- galaxy/tool-data/snpEff_genomes.loc.sample
- scripts_build/data/GRCh37.RefSeq/download_RefSeq_NCBI.sh
- scripts_build/data/GRCh38.RefSeq/download_RefSeq_NCBI.sh
- src/bds/download/downloadEnsemblBulk.bds
- src/bds/download/downloadGenome.bds
- src/bds/download/downloadMane.bds
- src/bds/download/downloadOther.bds
- src/bds/download/downloadUcsc.bds
- src/bds/make.bds
- src/docs/examples.md
- src/docs/index.html
- src/main/java/org/snpeff/SnpEff.java
- src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdBuild.java
- src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java
- src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdDatabases.java
- src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
- test_04_TestCasesEff.csv
Changes:
=====================================
README_release.md
=====================================
@@ -7,8 +7,10 @@
- Check `Config.DATABASE_COMPATIBLE_VERSIONS` for new version compatibilities added
2) Build JAR files: `./make.bds`
3) Run tests: `./make.bds -test`
-4) Upload core files to Azure: `./make.bds -uploadCore`
-5) Update web page and documentation: `./make.bds -createDocs`, see [Documentation section](#documentation)
+4) Run `SnpEff/git/reelease` and `SnpSift/git/reelease`
+5) Create distro ZIP files: `./make.bds -distroCore`
+6) Upload core files to Azure: `./make.bds -uploadCore`
+7) Update web page and documentation: `./make.bds -createDocs`, see [Documentation section](#documentation)
# Release process: Databases
=====================================
config/snpEff.ENSEMBL_105.config
=====================================
@@ -0,0 +1,1243 @@
+ASM210954v1.105.genome : Acanthochromis_polyacanthus
+ASM210954v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM210954v1.105.retrieval_date : 2022-04-11
+
+Accipiter_nisus_ver1.0.105.genome : Accipiter_nisus
+Accipiter_nisus_ver1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Accipiter_nisus_ver1.0.105.retrieval_date : 2022-04-11
+
+ASM200744v2.105.genome : Ailuropoda_melanoleuca
+ASM200744v2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM200744v2.105.retrieval_date : 2022-04-11
+
+ASM394721v1.105.genome : Amazona_collaria
+ASM394721v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM394721v1.105.retrieval_date : 2022-04-11
+
+Midas_v5.105.genome : Amphilophus_citrinellus
+Midas_v5.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Midas_v5.105.retrieval_date : 2022-04-11
+
+AmpOce1.0.105.genome : Amphiprion_ocellaris
+AmpOce1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+AmpOce1.0.105.retrieval_date : 2022-04-11
+
+Nemo_v1.105.genome : Amphiprion_percula
+Nemo_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Nemo_v1.105.retrieval_date : 2022-04-11
+
+fAnaTes1.2.105.genome : Anabas_testudineus
+fAnaTes1.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fAnaTes1.2.105.retrieval_date : 2022-04-11
+
+ASM874695v1.105.genome : Anas_platyrhynchos
+ASM874695v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM874695v1.105.retrieval_date : 2022-04-11
+
+CAU_duck1.0.105.genome : Anas_platyrhynchos_platyrhynchos
+CAU_duck1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CAU_duck1.0.105.retrieval_date : 2022-04-11
+
+ASM222487v1.105.genome : Anas_zonorhyncha
+ASM222487v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM222487v1.105.retrieval_date : 2022-04-11
+
+AnoCar2.0v2.105.genome : Anolis_carolinensis
+AnoCar2.0v2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+AnoCar2.0v2.105.retrieval_date : 2022-04-11
+
+ASM259213v1.105.genome : Anser_brachyrhynchus
+ASM259213v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM259213v1.105.retrieval_date : 2022-04-11
+
+GooseV1.0.105.genome : Anser_cygnoides
+GooseV1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+GooseV1.0.105.retrieval_date : 2022-04-11
+
+Anan_2.0.105.genome : Aotus_nancymaae
+Anan_2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Anan_2.0.105.retrieval_date : 2022-04-11
+
+aptHaa1.105.genome : Apteryx_haastii
+aptHaa1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+aptHaa1.105.retrieval_date : 2022-04-11
+
+aptOwe1.105.genome : Apteryx_owenii
+aptOwe1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+aptOwe1.105.retrieval_date : 2022-04-11
+
+aptRow1.105.genome : Apteryx_rowi
+aptRow1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+aptRow1.105.retrieval_date : 2022-04-11
+
+bAquChr1.2.105.genome : Aquila_chrysaetos_chrysaetos
+bAquChr1.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+bAquChr1.2.105.retrieval_date : 2022-04-11
+
+fAstCal1.2.105.genome : Astatotilapia_calliptera
+fAstCal1.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fAstCal1.2.105.retrieval_date : 2022-04-11
+
+Astyanax_mexicanus-2.0.105.genome : Astyanax_mexicanus
+Astyanax_mexicanus-2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Astyanax_mexicanus-2.0.105.retrieval_date : 2022-04-11
+
+Astyanax_mexicanus-1.0.2.105.genome : Astyanax_mexicanus_pachon
+Astyanax_mexicanus-1.0.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Astyanax_mexicanus-1.0.2.105.retrieval_date : 2022-04-11
+
+athCun1.105.genome : Athene_cunicularia
+athCun1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+athCun1.105.retrieval_date : 2022-04-11
+
+mBalMus1.v2.105.genome : Balaenoptera_musculus
+mBalMus1.v2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+mBalMus1.v2.105.retrieval_date : 2022-04-11
+
+fBetSpl5.2.105.genome : Betta_splendens
+fBetSpl5.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fBetSpl5.2.105.retrieval_date : 2022-04-11
+
+Bison_UMD1.0.105.genome : Bison_bison_bison
+Bison_UMD1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Bison_UMD1.0.105.retrieval_date : 2022-04-11
+
+LU_Bosgru_v3.0.105.genome : Bos_grunniens
+LU_Bosgru_v3.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+LU_Bosgru_v3.0.105.retrieval_date : 2022-04-11
+
+UOA_Brahman_1.105.genome : Bos_indicus_hybrid
+UOA_Brahman_1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+UOA_Brahman_1.105.retrieval_date : 2022-04-11
+
+BosGru_v2.0.105.genome : Bos_mutus
+BosGru_v2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+BosGru_v2.0.105.retrieval_date : 2022-04-11
+
+ARS-UCD1.2.105.genome : Bos_taurus
+ARS-UCD1.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ARS-UCD1.2.105.retrieval_date : 2022-04-11
+
+UOA_Angus_1.105.genome : Bos_taurus_hybrid
+UOA_Angus_1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+UOA_Angus_1.105.retrieval_date : 2022-04-11
+
+BubBub1.0.105.genome : Bubo_bubo
+BubBub1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+BubBub1.0.105.retrieval_date : 2022-04-11
+
+ButJap1.0.105.genome : Buteo_japonicus
+ButJap1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ButJap1.0.105.retrieval_date : 2022-04-11
+
+WBcel235.105.genome : Caenorhabditis_elegans
+WBcel235.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+WBcel235.105.retrieval_date : 2022-04-11
+
+CaiMos1.0.105.genome : Cairina_moschata_domestica
+CaiMos1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CaiMos1.0.105.retrieval_date : 2022-04-11
+
+ASM143184v1.105.genome : Calidris_pugnax
+ASM143184v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM143184v1.105.retrieval_date : 2022-04-11
+
+ASM369795v1.105.genome : Calidris_pygmaea
+ASM369795v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM369795v1.105.retrieval_date : 2022-04-11
+
+mCalJac1.pat.X.105.genome : Callithrix_jacchus
+mCalJac1.pat.X.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+mCalJac1.pat.X.105.retrieval_date : 2022-04-11
+
+Callorhinchus_milii-6.1.3.105.genome : Callorhinchus_milii
+Callorhinchus_milii-6.1.3.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Callorhinchus_milii-6.1.3.105.retrieval_date : 2022-04-11
+
+STF_HiC.105.genome : Camarhynchus_parvulus
+STF_HiC.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+STF_HiC.105.retrieval_date : 2022-04-11
+
+CamDro2.105.genome : Camelus_dromedarius
+CamDro2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CamDro2.105.retrieval_date : 2022-04-11
+
+ASM325472v1.105.genome : Canis_lupus_dingo
+ASM325472v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM325472v1.105.retrieval_date : 2022-04-11
+
+ROS_Cfam_1.0.105.genome : Canis_lupus_familiaris
+ROS_Cfam_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ROS_Cfam_1.0.105.retrieval_date : 2022-04-11
+
+Basenji_breed-1.1.105.genome : Canis_lupus_familiarisbasenji
+Basenji_breed-1.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Basenji_breed-1.1.105.retrieval_date : 2022-04-11
+
+Dog10K_Boxer_Tasha.105.genome : Canis_lupus_familiarisboxer
+Dog10K_Boxer_Tasha.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Dog10K_Boxer_Tasha.105.retrieval_date : 2022-04-11
+
+UMICH_Zoey_3.1.105.genome : Canis_lupus_familiarisgreatdane
+UMICH_Zoey_3.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+UMICH_Zoey_3.1.105.retrieval_date : 2022-04-11
+
+ARS1.105.genome : Capra_hircus
+ARS1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ARS1.105.retrieval_date : 2022-04-11
+
+CVASU_BBG_1.0.105.genome : Capra_hircus_blackbengal
+CVASU_BBG_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CVASU_BBG_1.0.105.retrieval_date : 2022-04-11
+
+ASM336829v1.105.genome : Carassius_auratus
+ASM336829v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM336829v1.105.retrieval_date : 2022-04-11
+
+Tarsius_syrichta-2.0.1.105.genome : Carlito_syrichta
+Tarsius_syrichta-2.0.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Tarsius_syrichta-2.0.1.105.retrieval_date : 2022-04-11
+
+C.can_genome_v1.0.105.genome : Castor_canadensis
+C.can_genome_v1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+C.can_genome_v1.0.105.retrieval_date : 2022-04-11
+
+CatWag_v2_BIUU_UCD.105.genome : Catagonus_wagneri
+CatWag_v2_BIUU_UCD.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CatWag_v2_BIUU_UCD.105.retrieval_date : 2022-04-11
+
+bCatUst1.pri.105.genome : Catharus_ustulatus
+bCatUst1.pri.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+bCatUst1.pri.105.retrieval_date : 2022-04-11
+
+CavAp1.0.105.genome : Cavia_aperea
+CavAp1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CavAp1.0.105.retrieval_date : 2022-04-11
+
+Cavpor3.0.105.genome : Cavia_porcellus
+Cavpor3.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Cavpor3.0.105.retrieval_date : 2022-04-11
+
+Cebus_imitator-1.0.105.genome : Cebus_capucinus
+Cebus_imitator-1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Cebus_imitator-1.0.105.retrieval_date : 2022-04-11
+
+Caty_1.0.105.genome : Cercocebus_atys
+Caty_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Caty_1.0.105.retrieval_date : 2022-04-11
+
+CEY_v1.105.genome : Cervus_hanglu_yarkandensis
+CEY_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CEY_v1.105.retrieval_date : 2022-04-11
+
+ASM359739v1.105.genome : Chelonoidis_abingdonii
+ASM359739v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM359739v1.105.retrieval_date : 2022-04-11
+
+Chelydra_serpentina-1.0.105.genome : Chelydra_serpentina
+Chelydra_serpentina-1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Chelydra_serpentina-1.0.105.retrieval_date : 2022-04-11
+
+ChiLan1.0.105.genome : Chinchilla_lanigera
+ChiLan1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ChiLan1.0.105.retrieval_date : 2022-04-11
+
+ChlSab1.1.105.genome : Chlorocebus_sabaeus
+ChlSab1.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ChlSab1.1.105.retrieval_date : 2022-04-11
+
+choHof1.105.genome : Choloepus_hoffmanni
+choHof1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+choHof1.105.retrieval_date : 2022-04-11
+
+Chrysemys_picta_bellii-3.0.3.105.genome : Chrysemys_picta_bellii
+Chrysemys_picta_bellii-3.0.3.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Chrysemys_picta_bellii-3.0.3.105.retrieval_date : 2022-04-11
+
+Chrysolophus_pictus_GenomeV1.0.105.genome : Chrysolophus_pictus
+Chrysolophus_pictus_GenomeV1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Chrysolophus_pictus_GenomeV1.0.105.retrieval_date : 2022-04-11
+
+KH.105.genome : Ciona_intestinalis
+KH.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+KH.105.retrieval_date : 2022-04-11
+
+CSAV2.0.105.genome : Ciona_savignyi
+CSAV2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CSAV2.0.105.retrieval_date : 2022-04-11
+
+Ch_v2.0.2.105.genome : Clupea_harengus
+Ch_v2.0.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Ch_v2.0.2.105.retrieval_date : 2022-04-11
+
+Cang.pa_1.0.105.genome : Colobus_angolensis_palliatus
+Cang.pa_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Cang.pa_1.0.105.retrieval_date : 2022-04-11
+
+UO_Cmon_1.0.105.genome : Corvus_moneduloides
+UO_Cmon_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+UO_Cmon_1.0.105.retrieval_date : 2022-04-11
+
+fCotGob3.1.105.genome : Cottoperca_gobio
+fCotGob3.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fCotGob3.1.105.retrieval_date : 2022-04-11
+
+Coturnix_japonica_2.0.105.genome : Coturnix_japonica
+Coturnix_japonica_2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Coturnix_japonica_2.0.105.retrieval_date : 2022-04-11
+
+CHOK1GS_HDv1.105.genome : Cricetulus_griseus_chok1gshd
+CHOK1GS_HDv1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CHOK1GS_HDv1.105.retrieval_date : 2022-04-11
+
+CriGri_1.0.105.genome : Cricetulus_griseus_crigri
+CriGri_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CriGri_1.0.105.retrieval_date : 2022-04-11
+
+CriGri-PICR.105.genome : Cricetulus_griseus_picr
+CriGri-PICR.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CriGri-PICR.105.retrieval_date : 2022-04-11
+
+CroPor_comp1.105.genome : Crocodylus_porosus
+CroPor_comp1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+CroPor_comp1.105.retrieval_date : 2022-04-11
+
+cyaCae2.105.genome : Cyanistes_caeruleus
+cyaCae2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+cyaCae2.105.retrieval_date : 2022-04-11
+
+fCycLum1.pri.105.genome : Cyclopterus_lumpus
+fCycLum1.pri.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fCycLum1.pri.105.retrieval_date : 2022-04-11
+
+Cse_v1.0.105.genome : Cynoglossus_semilaevis
+Cse_v1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Cse_v1.0.105.retrieval_date : 2022-04-11
+
+C_variegatus-1.0.105.genome : Cyprinodon_variegatus
+C_variegatus-1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+C_variegatus-1.0.105.retrieval_date : 2022-04-11
+
+common_carp_genome.105.genome : Cyprinus_carpio
+common_carp_genome.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+common_carp_genome.105.retrieval_date : 2022-04-11
+
+German_Mirror_carp_1.0.105.genome : Cyprinus_carpio_germanmirror
+German_Mirror_carp_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+German_Mirror_carp_1.0.105.retrieval_date : 2022-04-11
+
+Hebao_red_carp_1.0.105.genome : Cyprinus_carpio_hebaored
+Hebao_red_carp_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
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+C3H_HeJ_v1.105.genome : Mus_musculus_c3hhej
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+CAST_EiJ_v1.105.genome : Mus_musculus_casteij
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+DBA_2J_v1.105.genome : Mus_musculus_dba2j
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+FVB_NJ_v1.105.genome : Mus_musculus_fvbnj
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+NZO_HlLtJ_v1.105.genome : Mus_musculus_nzohlltj
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+PWK_PhJ_v1.105.genome : Mus_musculus_pwkphj
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+WSB_EiJ_v1.105.genome : Mus_musculus_wsbeij
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+PAHARI_EIJ_v1.1.105.genome : Mus_pahari
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+MUSP714.105.genome : Mus_spicilegus
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+SPRET_EiJ_v1.105.genome : Mus_spretus
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+fSpaAur1.1.105.genome : Sparus_aurata
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+ASM869450v1.105.genome : Stachyris_ruficeps
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+
+Stegastes_partitus-1.0.2.105.genome : Stegastes_partitus
+Stegastes_partitus-1.0.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Stegastes_partitus-1.0.2.105.retrieval_date : 2022-04-11
+
+bStrHab1_v1.p.105.genome : Strigops_habroptila
+bStrHab1_v1.p.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+bStrHab1_v1.p.105.retrieval_date : 2022-04-11
+
+Soccid_v01.105.genome : Strix_occidentalis_caurina
+Soccid_v01.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Soccid_v01.105.retrieval_date : 2022-04-11
+
+ASM69896v1.105.genome : Struthio_camelus_australis
+ASM69896v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM69896v1.105.retrieval_date : 2022-04-11
+
+meerkat_22Aug2017_6uvM2_HiC.105.genome : Suricata_suricatta
+meerkat_22Aug2017_6uvM2_HiC.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+meerkat_22Aug2017_6uvM2_HiC.105.retrieval_date : 2022-04-11
+
+Sscrofa11.1.105.genome : Sus_scrofa
+Sscrofa11.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Sscrofa11.1.105.retrieval_date : 2022-04-11
+
+Bamei_pig_v1.105.genome : Sus_scrofa_bamei
+Bamei_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Bamei_pig_v1.105.retrieval_date : 2022-04-11
+
+Berkshire_pig_v1.105.genome : Sus_scrofa_berkshire
+Berkshire_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Berkshire_pig_v1.105.retrieval_date : 2022-04-11
+
+Hampshire_pig_v1.105.genome : Sus_scrofa_hampshire
+Hampshire_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Hampshire_pig_v1.105.retrieval_date : 2022-04-11
+
+Jinhua_pig_v1.105.genome : Sus_scrofa_jinhua
+Jinhua_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Jinhua_pig_v1.105.retrieval_date : 2022-04-11
+
+Landrace_pig_v1.105.genome : Sus_scrofa_landrace
+Landrace_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Landrace_pig_v1.105.retrieval_date : 2022-04-11
+
+Large_White_v1.105.genome : Sus_scrofa_largewhite
+Large_White_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Large_White_v1.105.retrieval_date : 2022-04-11
+
+Meishan_pig_v1.105.genome : Sus_scrofa_meishan
+Meishan_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Meishan_pig_v1.105.retrieval_date : 2022-04-11
+
+Pietrain_pig_v1.105.genome : Sus_scrofa_pietrain
+Pietrain_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Pietrain_pig_v1.105.retrieval_date : 2022-04-11
+
+Rongchang_pig_v1.105.genome : Sus_scrofa_rongchang
+Rongchang_pig_v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Rongchang_pig_v1.105.retrieval_date : 2022-04-11
+
+Tibetan_Pig_v2.105.genome : Sus_scrofa_tibetan
+Tibetan_Pig_v2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Tibetan_Pig_v2.105.retrieval_date : 2022-04-11
+
+USMARCv1.0.105.genome : Sus_scrofa_usmarc
+USMARCv1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+USMARCv1.0.105.retrieval_date : 2022-04-11
+
+minipig_v1.0.105.genome : Sus_scrofa_wuzhishan
+minipig_v1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+minipig_v1.0.105.retrieval_date : 2022-04-11
+
+bTaeGut1_v1.p.105.genome : Taeniopygia_guttata
+bTaeGut1_v1.p.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+bTaeGut1_v1.p.105.retrieval_date : 2022-04-11
+
+fTakRub1.2.105.genome : Takifugu_rubripes
+fTakRub1.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+fTakRub1.2.105.retrieval_date : 2022-04-11
+
+T_m_triunguis-2.0.105.genome : Terrapene_carolina_triunguis
+T_m_triunguis-2.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+T_m_triunguis-2.0.105.retrieval_date : 2022-04-11
+
+TETRAODON8.105.genome : Tetraodon_nigroviridis
+TETRAODON8.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+TETRAODON8.105.retrieval_date : 2022-04-11
+
+Tgel_1.0.105.genome : Theropithecus_gelada
+Tgel_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Tgel_1.0.105.retrieval_date : 2022-04-11
+
+TREESHREW.105.genome : Tupaia_belangeri
+TREESHREW.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+TREESHREW.105.retrieval_date : 2022-04-11
+
+turTru1.105.genome : Tursiops_truncatus
+turTru1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+turTru1.105.retrieval_date : 2022-04-11
+
+ASM342692v1.105.genome : Urocitellus_parryii
+ASM342692v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM342692v1.105.retrieval_date : 2022-04-11
+
+ASM334442v1.105.genome : Ursus_americanus
+ASM334442v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM334442v1.105.retrieval_date : 2022-04-11
+
+UrsMar_1.0.105.genome : Ursus_maritimus
+UrsMar_1.0.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+UrsMar_1.0.105.retrieval_date : 2022-04-11
+
+ASM966005v1.105.genome : Ursus_thibetanus_thibetanus
+ASM966005v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM966005v1.105.retrieval_date : 2022-04-11
+
+ASM479886v1.105.genome : Varanus_komodoensis
+ASM479886v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM479886v1.105.retrieval_date : 2022-04-11
+
+vicPac1.105.genome : Vicugna_pacos
+vicPac1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+vicPac1.105.retrieval_date : 2022-04-11
+
+bare-nosed_wombat_genome_assembly.105.genome : Vombatus_ursinus
+bare-nosed_wombat_genome_assembly.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+bare-nosed_wombat_genome_assembly.105.retrieval_date : 2022-04-11
+
+VulVul2.2.105.genome : Vulpes_vulpes
+VulVul2.2.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+VulVul2.2.105.retrieval_date : 2022-04-11
+
+Xenopus_tropicalis_v9.1.105.genome : Xenopus_tropicalis
+Xenopus_tropicalis_v9.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Xenopus_tropicalis_v9.1.105.retrieval_date : 2022-04-11
+
+Xiphophorus_couchianus-4.0.1.105.genome : Xiphophorus_couchianus
+Xiphophorus_couchianus-4.0.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Xiphophorus_couchianus-4.0.1.105.retrieval_date : 2022-04-11
+
+X_maculatus-5.0-male.105.genome : Xiphophorus_maculatus
+X_maculatus-5.0-male.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+X_maculatus-5.0-male.105.retrieval_date : 2022-04-11
+
+mZalCal1.pri.105.genome : Zalophus_californianus
+mZalCal1.pri.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+mZalCal1.pri.105.retrieval_date : 2022-04-11
+
+Zonotrichia_albicollis-1.0.1.105.genome : Zonotrichia_albicollis
+Zonotrichia_albicollis-1.0.1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+Zonotrichia_albicollis-1.0.1.105.retrieval_date : 2022-04-11
+
+ASM128173v1.105.genome : Zosterops_lateralis_melanops
+ASM128173v1.105.reference : ftp://ftp.ensembl.org/pub/release-105/gtf/
+ASM128173v1.105.retrieval_date : 2022-04-11
=====================================
config/snpEff.ENSEMBL_BFMPP_52.config
=====================================
The diff for this file was not included because it is too large.
=====================================
config/snpEff.FLYBASE_FB2022_02.config
=====================================
@@ -0,0 +1,2 @@
+
+dmel_r6.45.genome: dmel_r6.45
=====================================
config/snpEff.config
=====================================
The diff for this file was not included because it is too large.
=====================================
config/snpEff.dbs.config
=====================================
@@ -58,12 +58,18 @@ GRCh37.p13.reference : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/
GRCh37.p13.M.codonTable : Vertebrate_Mitochondrial
GRCh37.p13.MT.codonTable : Vertebrate_Mitochondrial
-# GRCh38 release from NCBI's RefSeq
+# GRCh38 release 'p14' from NCBI's RefSeq
GRCh38.p13.genome : Human genome GRCh38 using RefSeq transcripts
GRCh38.p13.reference : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/
GRCh38.p13.M.codonTable : Vertebrate_Mitochondrial
GRCh38.p13.MT.codonTable : Vertebrate_Mitochondrial
+# GRCh38 release 'p14' from NCBI's RefSeq
+GRCh38.p14.genome : Human genome GRCh38 using RefSeq transcripts
+GRCh38.p14.reference : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p14/
+ GRCh38.p14.M.codonTable : Vertebrate_Mitochondrial
+ GRCh38.p14.MT.codonTable : Vertebrate_Mitochondrial
+
# MANE
GRCh38.mane.0.95.ensembl.genome: Human genome GRCh38, using MANE transcripts v0.95, Ensembl IDs
GRCh38.GRCh38.mane.0.95.ensembl.M.codonTable : Vertebrate_Mitochondrial
@@ -73,6 +79,14 @@ GRCh38.mane.0.95.refseq.genome: Human genome GRCh38, using MANE transcripts v0.9
GRCh38.GRCh38.mane.0.95.refseq.M.codonTable : Vertebrate_Mitochondrial
GRCh38.GRCh38.mane.0.95.refseq.MT.codonTable : Vertebrate_Mitochondrial
+GRCh38.mane.1.0.ensembl.genome: Human genome GRCh38, using MANE transcripts v1.0, Ensembl IDs
+ GRCh38.GRCh38.mane.1.0.ensembl.M.codonTable : Vertebrate_Mitochondrial
+ GRCh38.GRCh38.mane.1.0.ensembl.MT.codonTable : Vertebrate_Mitochondrial
+
+GRCh38.mane.1.0.refseq.genome: Human genome GRCh38, using MANE transcripts v1.0, RefSeq IDs
+ GRCh38.GRCh38.mane.1.0.refseq.M.codonTable : Vertebrate_Mitochondrial
+ GRCh38.GRCh38.mane.1.0.refseq.MT.codonTable : Vertebrate_Mitochondrial
+
# Mouse
mm9.genome : Mouse
mm10.genome : Mouse
=====================================
docs/examples/index.html
=====================================
@@ -1505,7 +1505,7 @@ We highly recommend reading their comprehensive documentation available <a href=
cd
# Download and install SnpEff
-curl -v -L 'https://datasetsnpeff.blob.core.windows.net/dataset/versions/snpEff_latest_core.zip?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D' > snpEff_latest_core.zip
+curl -v -L 'https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip' > snpEff_latest_core.zip
unzip snpEff_latest_core.zip
</code></pre>
<p><strong>Notes:</strong></p>
=====================================
docs/index.html
=====================================
@@ -113,7 +113,7 @@
<br>
<div class="row-fluid">
<div class="span4">
- <a href="https://datasetsnpeff.blob.core.windows.net/dataset/versions/snpEff_latest_core.zip?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D" class="btn btn-primary btn-large" onClick="ga('send', 'event', { eventCategory: 'download', eventAction: 'snpeff_core'});">Download SnpEff</a>
+ <a href="https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip" class="btn btn-primary btn-large" onClick="ga('send', 'event', { eventCategory: 'download', eventAction: 'snpeff_core'});">Download SnpEff</a>
<br>
Latest version 5.1 (2022-01-21)<br>
Requires Java 12<br>
=====================================
docs/sitemap.xml.gz
=====================================
Binary files a/docs/sitemap.xml.gz and b/docs/sitemap.xml.gz differ
=====================================
docs/versions.txt
=====================================
@@ -1 +1 @@
-SNPEFF 5.0E 2021-03-09 https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
+SNPEFF 5.1D 2022-04-19 https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
=====================================
galaxy/tool-data/snpEff_genomes.loc
=====================================
The diff for this file was not included because it is too large.
=====================================
galaxy/tool-data/snpEff_genomes.loc.sample
=====================================
The diff for this file was not included because it is too large.
=====================================
scripts_build/data/GRCh37.RefSeq/download_RefSeq_NCBI.sh
=====================================
@@ -10,7 +10,7 @@ VER="GRCh37"
SUBVER="p13"
ASSEMBLY_ID="GCF_000001405.25"
RELEASE="105.20190906"
-GENOME="$VER.$SUBVER.RefSeq"
+GENOME="$VER.$SUBVER"
# Path to scripts
SNPEFF_DIR="$HOME/snpEff"
@@ -82,11 +82,11 @@ echo "Processing protein FASTA files"
gunzip -c "$PROT_FASTA_ORI" | $SCRIPTS_BUILD_DIR/fix_fasta_protein_cds.pl protein_id.map.txt > "$DB_DIR/protein.fa"
echo "Processing RNA FASTA files"
-gunzip -c "$RNA_FASTA_ORI" | perl -pe 's/^>(\S+).*/>$1/' > "$DB_DIR/mrna.fa"
+gunzip -c "$RNA_FASTA_ORI" | perl -pe 's/^>(\S+).*/>$1/' > "$DB_DIR/cds.fa"
#---
# Compress
#---
-pigz -v genes.gtf mrna.fa protein.fa protein_id.map.txt sequences.fa
+pigz -v genes.gtf cds.fa protein.fa protein_id.map.txt sequences.fa
echo "Done."
=====================================
scripts_build/data/GRCh38.RefSeq/download_RefSeq_NCBI.sh
=====================================
@@ -7,10 +7,19 @@ PROGRAM_DIR=$(cd $(dirname $0); pwd -P)
# https://ftp.ncbi.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/annotation_releases/109.20200815/
VER="GRCh38"
+
+# Latest version
+SUBVER="p14"
+ASSEMBLY_ID="GCF_000001405.40"
+RELEASE="110"
+
+# Previous version
SUBVER="p13"
ASSEMBLY_ID="GCF_000001405.39"
RELEASE="109.20200815"
-GENOME="$VER.$SUBVER.RefSeq"
+RELEASE="109.20211119"
+
+GENOME="$VER.$SUBVER"
# Path to scripts
SNPEFF_DIR="$HOME/snpEff"
@@ -82,11 +91,11 @@ echo "Processing protein FASTA files"
gunzip -c "$PROT_FASTA_ORI" | $SCRIPTS_BUILD_DIR/fix_fasta_protein_cds.pl protein_id.map.txt > "$DB_DIR/protein.fa"
echo "Processing RNA FASTA files"
-gunzip -c "$RNA_FASTA_ORI" | perl -pe 's/^>(\S+).*/>$1/' > "$DB_DIR/mrna.fa"
+gunzip -c "$RNA_FASTA_ORI" | perl -pe 's/^>(\S+).*/>$1/' > "$DB_DIR/cds.fa"
#---
# Compress
#---
-pigz -v genes.gtf mrna.fa protein.fa protein_id.map.txt sequences.fa
+pigz -v genes.gtf cds.fa protein.fa protein_id.map.txt sequences.fa
echo "Done."
=====================================
src/bds/download/downloadEnsemblBulk.bds
=====================================
@@ -269,11 +269,11 @@ void downloadEnsemblBfmpp() {
# Move files to propper structure in 'local data' dir
#---
# Copy files to local dir
- println "ENSEMBL BFMPP $ensemblBfmppRelease: Copying files to parent dir"
+ log("ENSEMBL BFMPP $ensemblBfmppRelease: Copying files to parent dir")
sys find . -mindepth 2 -type f -not -path "*/data/*" | xargs -I + $cp + .
# Move files
- println "ENSEMBL BFMPP $ensemblBfmppRelease: Copying files to data dir"
+ log("ENSEMBL BFMPP $ensemblBfmppRelease: Copying files to data dir")
string[] configLines
today := sys date +"%Y-%m-%d"
for( string gtf : ".".dir("*.gtf.gz") ) {
@@ -281,7 +281,7 @@ void downloadEnsemblBfmpp() {
baseNoVer := base.removeExt()
longName := base.split('\.').head()
name := longName
- println "name: $name\tbase: $base"
+ log("ENSEMBL BFMPP $ensemblBfmppRelease: '$name'\tbase: '$base'")
if( name.isEmpty() ) continue
fasta := "$baseNoVer\.dna.toplevel.fa.gz"
@@ -304,10 +304,10 @@ void downloadEnsemblBfmpp() {
}
# Create config file
- if( configFile.exists() ) {
- println "WARNING: Config file exists, skipping ('$configFile')"
+ if( configFile.exists() && configFile.size() > 0) {
+ warning("ENSEMBL BFMPP $ensemblBfmppRelease: Config file '$configFile' exists, skipping")
} else {
- println "ENSEMBL BFMPP $ensemblBfmppRelease: Writing config file $configFile"
+ log("ENSEMBL BFMPP $ensemblBfmppRelease: Creating config file '$configFile'")
configFile.write( configLines.join("\n") )
}
=====================================
src/bds/download/downloadGenome.bds
=====================================
@@ -19,16 +19,17 @@ class DownloadGenome {
dirDataGenome = "$dirData/$genome"
# Get class (short) name to infer download dir (remove the 'Download' prefix to the class name)
- #className = type(this).toLower()
- #if( className.startsWith('download') ) className = className.substr('download'.length())
+ className = type(this).toLower()
+ if( className.startsWith('download') ) className = className.substr('download'.length())
downloadDir = "$dirDownload/$className/$genome"
+ log("Download dir: '$downloadDir'")
# Genome name without version number
setGenomeAndVersion()
}
- # If the referce FASTA file 'fastaDataEq' exists, create a link
+ # If the reference FASTA file 'fastaDataEq' exists, create a link
void checkRefrenceFasta() {
if( !fastaDataEq.exists() || fastaData.exists() ) return
log("Download '$genome': FASTA refernce file '$fastaDataEq' exists, linking")
@@ -75,11 +76,11 @@ class DownloadGenome {
# Download (and build) 'cds' FASTA file to local download dir
# Returns: Path to file
string downloadCdsFastaCheck() {
- if( cdsData.exists() ) {
+ if( isDownloaded(cdsData) ) {
log("Download CDS FASTA: Data file '$cdsData' already exists, skipping")
return ''
}
- if( cdsLocal.exists() ) {
+ if( isDownloaded(cdsLocal) ) {
log("Download CDS FASTA: Data file '$cdsLocal' already exists, skipping")
return cdsLocal
}
@@ -94,11 +95,11 @@ class DownloadGenome {
# Download (and build) reference genome FASTA file to local download dir
# Returns: Path to fasta file or empty if no download is needed
string downloadFastaCheck() {
- if( fastaData.exists() ) {
+ if( isDownloaded(fastaData) ) {
log("Download Reference FASTA: Data file '$fastaData' already exists, skipping")
return ''
}
- if( fastaLocal.exists() ) {
+ if( isDownloaded(fastaLocal) ) {
log("Download Reference FASTA: Data file '$fastaLocal' already exists, skipping")
return fastaLocal
}
@@ -113,10 +114,10 @@ class DownloadGenome {
return ''
}
if( localFile.isEmpty() ) {
- log("Downloading '$genome' $title: Empty local file, skipping")
+ log("Downloading '$genome' $title: Empty local file name, skipping")
return ''
}
- if( localFile.exists() ) {
+ if( isDownloaded(localFile) ) {
println "Local file '$localFile' exists, skipping download"
return localFile
}
@@ -133,12 +134,12 @@ class DownloadGenome {
# Download (and build) 'genes' file to local download dir
# Returns: Path to file (GTF, GFF, RefSeq, GeneBank, etc.)
string downloadGenesCheck() {
- if( genesData.exists() ) {
+ if( isDownloaded(genesData) ) {
log("Download Genes: Data file '$genesData' already exists, skipping")
return ''
}
- if( genesLocal.exists() ) {
- log("Download Genes: Data file '$genesLocal' already exists, skipping")
+ if( isDownloaded(genesLocal) ) {
+ log("Download Genes: Data local file '$genesLocal' already exists, skipping")
return genesLocal
}
@@ -161,12 +162,12 @@ class DownloadGenome {
# Download (and build) 'protein' FASTA file to local download dir
# Returns: Path to file
string downloadProteinFastaCheck() {
- if( protData.exists() ) {
- log("Download Protein FASTA: Data file '$protData' already exists, skipping")
+ if( isDownloaded(protData) ) {
+ log("Download Protein FASTA: Data file '$protData' already exists or empty, skipping")
return ''
}
- if( protLocal.exists() ) {
- log("Download Protein FASTA: Data file '$protLocal' already exists, skipping")
+ if( isDownloaded(protLocal) ) {
+ log("Download Protein FASTA: Local file '$protLocal' already exists or empty, skipping")
return protLocal
}
return downloadProteinFasta()
@@ -185,7 +186,7 @@ class DownloadGenome {
if( fastaData.isEmpty() ) fastaData = "$dirData/genomes/$genome\.fa.gz"
if( fastaDataEq.isEmpty() ) fastaDataEq = "$dirData/genomes/$genomeNoVer\.fa.gz"
if( cdsData.isEmpty() ) cdsData = dirDataGenome + "/cds.fa.gz"
- if( protData.isEmpty() ) protData = dirDataGenome + "/proteing.fa.gz"
+ if( protData.isEmpty() ) protData = dirDataGenome + "/protein.fa.gz"
dirDataGenome.mkdir()
downloadDir.mkdir()
@@ -200,6 +201,11 @@ class DownloadGenome {
task( dst <- src ) sys cp -vf '$src' '$dst'
}
+ # Retrun true if the (local) file has already been downloaded (exists and non-empty)
+ bool isDownloaded(string path) {
+ return path.exists() && (path.size() > 0)
+ }
+
# Pre-Process (default, do nothing)
void preProcess() return
=====================================
src/bds/download/downloadMane.bds
=====================================
@@ -9,8 +9,10 @@
urlMane := "https://ftp.ncbi.nlm.nih.gov/refseq/MANE/MANE_human/"
void downloadManeGenome() {
- dg := new DownloadMane(maneGenome, maneRelease, maneTrIdType)
- dg.download()
+ for(string maneTrIdType: maneTrIdTypes) {
+ dg := new DownloadMane(maneGenome, maneRelease, maneTrIdType)
+ dg.download()
+ }
}
@@ -27,10 +29,10 @@ class DownloadMane extends DownloadGenome {
log("Downloading MANE '$genome': release '$release', transcript type '$trType', to '$downloadDir'")
# Download from NCBI's MANE site
- urlBase := "$urlMane/release_$release"
- cdsUrl = "$urlBase/MANE.$genome\.v$release\.select_$trType\_rna.fna.gz"
- genesUrl = "$urlBase/MANE.$genome\.v$release\.select_$trType\_genomic.gtf.gz"
- protUrl = "$urlBase/MANE.$genome\.v$release\.select_$trType\_protein.faa.gz"
+ urlBase := "$urlMane/release_$release/MANE.$genome\.v$release\." + (maneSelect ? "select_" : "") + trType
+ cdsUrl = "$urlBase\_rna.fna.gz"
+ genesUrl = "$urlBase\_genomic.gtf.gz"
+ protUrl = "$urlBase\_protein.faa.gz"
# Download genome reference from NCBI
urlEnsemblBase := "http://ftp.ensembl.org/pub/release-$ensemblRelease"
=====================================
src/bds/download/downloadOther.bds
=====================================
@@ -6,7 +6,7 @@
#
#-------------------------------------------------------------------------------
-urlFlyBase := "ftp://ftp.flybase.net"
+urlFlyBase := "https://ftp.flybase.net"
#-------------------------------------------------------------------------------
# Download FlyBase
=====================================
src/bds/download/downloadUcsc.bds
=====================================
@@ -26,33 +26,37 @@ void downloadUcscGenome(string genome) {
# Class to download files and query MySql database from UCSC
class DownloadUcsc extends DownloadGenome {
+ string fastaUrl
string fastaTarUrl
string cytoBandUrl
- string cdsUrlAlt
- string genesUrlAlt
+ string[] cdsUrls
+ string[] genesUrls
void DownloadUcsc(string genome) {
super.DownloadGenome(genome)
cdsUrl = "$urlUcscSoe/$genome/bigZips/refMrna.fa.gz"
- cdsUrlAlt = "$urlUcscSoe/$genome/bigZips/mrna.fa.gz"
+ cdsUrls = [cdsUrl, "$urlUcscSoe/$genome/bigZips/mrna.fa.gz"]
fastaUrl = "$urlUcscCse/$genome/bigZips/$genome\.fa.gz"
fastaTarUrl = "$urlUcscCse/$genome/bigZips/chromFa.tar.gz"
genesUrl = "$urlUcscSoe/$genome/bigZips/genes/$genome\.refGene.gtf.gz"
- genesUrlAlt = "$urlUcscSoe/$genome/bigZips/genes/$genome\.ncbiRefSeq.gtf.gz"
+ genesUrls = [genesUrl, "$urlUcscSoe/$genome/bigZips/genes/$genome\.ncbiRefSeq.gtf.gz"]
cytoBandUrl = "$urlUcscCse/$genome/database/cytoBand.txt.gz"
protUrl = '' # It looks like there is no protein file with RefSeq transcripts at this moment
}
string downloadCdsFasta() {
- if( cdsUrl.exists() ) return downloadFile(cdsUrl, cdsLocal, "CDS FASTA", false)
- if( cdsUrlAlt.exists() ) return downloadFile(cdsUrlAlt, cdsLocal, "CDS FASTA", false)
- error "Could not find CDS / mRNA FASTA file"
+ for(string cdsUrl: cdsUrls) {
+ log("Downloading CDS FASTA '$cdsUrl'")
+ if( cdsUrl.exists() ) return downloadFile(cdsUrl, cdsLocal, "CDS FASTA", false)
+ else log("WARNING: Could not download CDS FASTA '$cdsUrl'")
+ }
+ error "Could not find CDS / mRNA FASTA file from any of $cdsUrls"
}
string downloadCytoBand() {
cytoBandFile := "$downloadDir/cytoBand.txt.gz"
if( !cytoBandFile.exists() && cytoBandUrl.exists() ) {
- wget(cytoBandUrl, cytoBandFile)
+ wget(cytoBandUrl, cytoBandFile, true, true, false)
return cytoBandFile
}
return '';
@@ -67,7 +71,7 @@ class DownloadUcsc extends DownloadGenome {
wgetTask(fastaTarUrl, localTar)
fastaLocal = fastaFromTar(localTar) # Create fasta from tar
} else {
- println "Could not download FASTA reference genome file\n\tFASTA: '$fastaUrl'\n\tTAR: '$fastaTarUrl'"
+ log("Could not download FASTA reference genome file\n\tFASTA: '$fastaUrl'\n\tTAR: '$fastaTarUrl'")
}
return fastaLocal
@@ -86,9 +90,13 @@ class DownloadUcsc extends DownloadGenome {
# Download geome from UCSC, ony if it has a GTF file
string downloadGtf() {
log("Downloading '$genome' (UCSC): GTF file")
- if( genesUrl.exists() ) return wgetTask(genesUrl, genesLocal) ? genesLocal : ''
- if( genesUrlAlt.exists() ) return wgetTask(genesUrlAlt, genesLocal) ? genesLocal : ''
- error "Could not download genes from '$genesUrl' or '$genesUrlAlt'"
+ for(string genesUrl: genesUrls) {
+ log("Downloading Genes file '$genesUrl'")
+ if( genesUrl.exists() ) return downloadFile(genesUrl, genesLocal, "Genes GTF", true)
+ else log("WARNING: Could not download Genes file '$genesUrl'")
+ }
+ log("Could not download genes from any of: $genesUrls")
+ return ''
}
string downloadProteinFasta() {
@@ -116,7 +124,7 @@ class DownloadUcsc extends DownloadGenome {
sys cd '$dirChr'
sys tar -xvzf '$tar'
sys rm -f '$fasta'
- sys cat `find . -iname "*.fa"` | gzip -c > 'fasta'
+ sys cat `find . -iname "*.fa"` | gzip -c > '$fasta'
}
return fasta
@@ -203,7 +211,6 @@ class DownloadUcsc extends DownloadGenome {
}
}
-
# Download a 'knaownGenes' version of the genome
class DownloadUcscKg extends DownloadUcsc {
string refdb
=====================================
src/bds/make.bds
=====================================
@@ -53,8 +53,9 @@ ensemblReleases := [ensemblRelease]
help MANE
downloadMane := false help Download MANE
maneGenome := 'GRCh38' help MANE genome
-maneRelease := '0.95' help MANE release version
-maneTrIdType := 'ensembl' help MANE release transcript ID type: {'ensembl', 'refseq'}
+maneRelease := '1.0' help MANE release version
+maneSelect := false help MANE 'select' or regular version
+maneTrIdTypes := ['ensembl', 'refseq'] help MANE release transcript ID type: {'ensembl', 'refseq'}
help UCSC
downloadUcsc := '' help Download genome files from UCSC (genome name)
@@ -64,9 +65,9 @@ downloadNcbi := '' help Download genome files from NCBI (both 'genome name' a
ncbiId := '' help Download genome ID from NCBI (both 'genome name' and 'genome ID' are required)
help Flybase
-flybaseRelease := "FB2021_06" help Flybase release
+flybaseRelease := "FB2022_02" help Flybase release
#flybaseGenomes := [ 'dana_r1.06', 'dere_r1.05', 'dgri_r1.05', 'dmel_r6.43', 'dmoj_r1.04', 'dper_r1.3', 'dpse_r3.04', 'dsec_r1.3', 'dsim_r2.02', 'dvir_r1.07', 'dwil_r1.05', 'dyak_r1.05' ]
-flybaseGenomes := [ 'dmel_r6.43'] # Note: It looks like FlyBase is not providing any GTF files for other than 'dmel', this is really weird, they used to have them in the past (maybe the project is dead/dying?)
+flybaseGenomes := [ 'dmel_r6.45'] # Note: It looks like FlyBase is not providing any GTF files for other than 'dmel', this is really weird, they used to have them in the past (maybe the project is dead/dying?)
# Human
GRCH := "GRCh38"
@@ -76,9 +77,10 @@ humanChrs := [ '1', '2', '3', '4', '5', '6', '7', '8', '9', '10', '11', '12',
humanChrsDd := [ '01', '02', '03', '04', '05', '06', '07', '08', '09', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '21', '22', 'X', 'Y', 'MT']
dbNsfpVersion := '4.2a'
# UCSC full list of genomes from "curl ftp://hgdownload.cse.ucsc.edu/goldenPath/"
-ucscGenomes := ['ailMel1', 'allMis1', 'anoCar2', 'anoGam3', 'apiMel2', 'aplCal1', 'aptMan1', 'balAcu1', 'bisBis1', 'bosTau9', 'braFlo1', 'caeJap1', 'caePb2', 'caeRem3', 'calJac4', 'calMil1', 'canFam6', 'cavPor3', 'cb3', 'ce11', 'ce2', 'ce4', 'ce6', 'cerSim1', 'chlSab2', 'choHof1', 'chrPic1', 'ci3', 'criGri1', 'criGriChoV1', 'criGriChoV2', 'danRer11', 'dasNov3', 'dipOrd1', 'dm6', 'dp3', 'droAna2', 'droEre1', 'droGri1', 'droMoj2', 'droPer1', 'droSec1', 'droSim1', 'droVir2', 'droYak2', 'eboVir3', 'echTel2', 'enhLutNer1', 'equCab3', 'eriEur2', 'felCat9', 'fr3', 'gadMor1', 'galGal6', 'galVar1', 'gasAcu1', 'geoFor1', 'gorGor6', 'hetGla2', 'hg19', 'hg38', 'latCha1', 'loxAfr3', 'macEug2', 'macFas5', 'manPen1', 'melGal5', 'melUnd1', 'micMur2', 'mm9', 'mm10', 'mm39', 'mm9', 'monDom5', 'musFur1', 'nanPar1', 'nasLar1', 'neoSch1', 'nomLeu3', 'ochPri3', 'oreNil2', 'ornAna2', 'oryCun2', 'oryLat2', 'otoGar3', 'oviAri4', 'panPan3', 'panTro6', 'papAnu4', 'papHam1', 'petMar3', 'ponAbe3', 'proCap1', 'pteVam1', 'rheMac10', 'rhiRox1', 'rn7', 'sacCer3', 'saiBol1', 'sarHar1', 'sorAra2', 'speTri2', 'strPur2', 'susScr11', 'taeGut2', 'tarSyr2', 'tetNig2', 'thaSir1', 'triMan1', 'tupBel1', 'turTru2', 'vicPac2', 'wuhCor1', 'xenLae2', 'xenTro10' ]
+ucscGenomes := ['ailMel1', 'allMis1', 'anoCar2', 'anoGam3', 'apiMel2', 'aplCal1', 'aptMan1', 'bisBis1', 'bosTau9', 'braFlo1', 'caeJap1', 'caePb2', 'caeRem3', 'calJac4', 'calMil1', 'cavPor3', 'cb3', 'ce11', 'ce2', 'ce4', 'ce6', 'cerSim1', 'chlSab2', 'choHof1', 'chrPic1', 'ci3', 'criGri1', 'criGriChoV1', 'criGriChoV2', 'danRer11', 'dasNov3', 'dipOrd1', 'dm6', 'dp3', 'droAna2', 'droEre1', 'droMoj2', 'droPer1', 'droSec1', 'droSim1', 'droVir2', 'droYak2', 'eboVir3', 'echTel2', 'enhLutNer1', 'equCab3', 'eriEur2', 'felCat9', 'fr3', 'gadMor1', 'galGal6', 'galVar1', 'gasAcu1', 'geoFor1', 'gorGor6', 'hetGla2', 'hg19', 'hg38', 'latCha1', 'loxAfr3', 'macEug2', 'macFas5', 'manPen1', 'melGal5', 'melUnd1', 'micMur2', 'mm9', 'mm10', 'mm39', 'mm9', 'monDom5', 'musFur1', 'nanPar1', 'nasLar1', 'neoSch1', 'nomLeu3', 'ochPri3', 'oreNil2', 'ornAna2', 'oryCun2', 'oryLat2', 'otoGar3', 'oviAri4', 'panPan3', 'panTro6', 'papAnu4', 'papHam1', 'petMar3', 'ponAbe3', 'proCap1', 'pteVam1', 'rheMac10', 'rhiRox1', 'rn7', 'sacCer3', 'saiBol1', 'sarHar1', 'sorAra2', 'speTri2', 'strPur2', 'susScr11', 'taeGut2', 'tarSyr2', 'tetNig2', 'thaSir1', 'triMan1', 'tupBel1', 'turTru2', 'vicPac2', 'wuhCor1', 'xenLae2', 'xenTro10']
# Removed:
# aquChr2: Missing CDS fasta
+# balAcu1: Missing CDS fasta
ucscGenomesRefGene := [ 'hg19', 'hg38', 'mm9', 'mm10', 'mm39' ]
ucscGenomesKg := [ 'hg19', 'hg38', 'mm9', 'mm10', 'mm39' ]
@@ -139,26 +141,29 @@ snpEffVersion := ""
bool addBuildDb(string genome) {
dir := "$dirData/$genome"
db := "$dir/snpEffectPredictor.bin"
- geneFiles := dir.dirPath("**/genes.*")
+ geneFiles := dir.dirPath("**/genes.*")
+ logfile := "$dirBuild/build.$genome\.out"
# No 'genes' file? Error
if( geneFiles.isEmpty() ) {
- warning("No genes file for $genome\n")
+ warning("No genes file for '$genome', skipping")
return( false );
}
geneFile := geneFiles.head()
if( built.hasKey(genome) ) {
- log("Genome $genome already built\n")
+ log("DONE: Genome '$genome' already built, skipping")
+ } else if( logfile.exists() ) {
+ log("DONE: Genome '$genome', log file '$logfile' already exists, skipping")
} else if( db <- geneFile ) {
- print("BUILD:\t$genome\tgeneFile: $geneFile\tdb: $db\n")
+ log("BUILD:\t$genome\tgeneFile: $geneFile\tdb: $db\n")
# Use 'storeSeqs' for human and mouse genome
opt := ( genome.startsWith('GRC') || genome.startsWith('hg') ? "-storeSeqs" : "" )
- task $snpeffBuild $opt $genome 2>&1 | tee $dirBuild/build.$genome\.out
+ task $snpeffBuild $opt $genome 2>&1 | tee '$logfile'
} else {
- print("OK :\t$genome\tgeneFile: $geneFile\tdb: $db\n")
+ log("DONE :\t$genome\tgeneFile: $geneFile\tdb: $db")
}
# Mark as built
@@ -307,7 +312,7 @@ bool buildDbAll() {
# Look into all directories
print("Available databases:\n")
- dbids := sys $snpeff databases | cut -f 1 | tail -n +3
+ dbids := sys $snpeff databases | grep -v "^URL" | cut -f 1 | tail -n +3
print("Building:\n")
for(string genome : dbids.lines() ) {
=====================================
src/docs/examples.md
=====================================
@@ -24,7 +24,7 @@ Before starting the protocol, it is necessary to download and install SnpEff. To
cd
# Download and install SnpEff
-curl -v -L 'https://datasetsnpeff.blob.core.windows.net/dataset/versions/snpEff_latest_core.zip?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D' > snpEff_latest_core.zip
+curl -v -L 'https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip' > snpEff_latest_core.zip
unzip snpEff_latest_core.zip
```
=====================================
src/docs/index.html
=====================================
@@ -113,7 +113,7 @@
<br>
<div class="row-fluid">
<div class="span4">
- <a href="https://datasetsnpeff.blob.core.windows.net/dataset/versions/snpEff_latest_core.zip?sv=2019-10-10&st=2020-09-01T00%3A00%3A00Z&se=2050-09-01T00%3A00%3A00Z&si=prod&sr=c&sig=isafOa9tGnYBAvsXFUMDGMTbsG2z%2FShaihzp7JE5dHw%3D" class="btn btn-primary btn-large" onClick="ga('send', 'event', { eventCategory: 'download', eventAction: 'snpeff_core'});">Download SnpEff</a>
+ <a href="https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip" class="btn btn-primary btn-large" onClick="ga('send', 'event', { eventCategory: 'download', eventAction: 'snpeff_core'});">Download SnpEff</a>
<br>
Latest version 5.1 (2022-01-21)<br>
Requires Java 12<br>
=====================================
src/main/java/org/snpeff/SnpEff.java
=====================================
@@ -93,7 +93,7 @@ public class SnpEff implements CommandLine {
// Version info
public static final String SOFTWARE_NAME = "SnpEff";
- public static final String REVISION = "";
+ public static final String REVISION = "d";
public static final String BUILD = Gpr.compileTimeStamp(SnpEff.class);
public static final String BUILD_DATE = Gpr.compileDate(SnpEff.class);
public static final String VERSION_MAJOR = "5.1";
=====================================
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdBuild.java
=====================================
@@ -38,6 +38,7 @@ public class SnpEffCmdBuild extends SnpEff {
boolean storeSequences = true; // Store full sequences
boolean regSortedByType = false;
String cellType = null;
+ double maxErrorRate = -1;
SnpEffCmdProtein snpEffCmdProtein;
SnpEffCmdCds snpEffCmdCds;
@@ -66,7 +67,11 @@ public class SnpEffCmdBuild extends SnpEff {
boolean checkDbCds(SnpEffPredictorFactory snpEffectPredictorFactory) {
var okCds = false;
String cdsFile = config.getFileNameCds();
- if (Gpr.canRead(cdsFile)) {
+ if (geneDatabaseFormat == GeneDatabaseFormat.GENBANK) {
+ // GenBank format
+ if (verbose) Log.info("CDS check: GenBank file format, skipping\n");
+ okCds = true;
+ } else if (Gpr.canRead(cdsFile)) {
// Use FASTA format
if (verbose) Log.info("CDS check (FASTA file): '" + cdsFile + "'\n");
snpEffCmdCds = new SnpEffCmdCds(config);
@@ -74,6 +79,7 @@ public class SnpEffCmdBuild extends SnpEff {
snpEffCmdCds.setDebug(debug);
snpEffCmdCds.setStoreAlignments(storeAlignments);
snpEffCmdCds.setCheckNumOk(checkNumOk);
+ if( maxErrorRate >= 0) snpEffCmdCds.setMaxErrorRate(maxErrorRate);
okCds = snpEffCmdCds.run();
if (!okCds && verbose) Log.info("\tCDS sequences comparison failed!");
} else Log.error("CDS check file '" + cdsFile + "' not found.");
@@ -109,6 +115,7 @@ public class SnpEffCmdBuild extends SnpEff {
snpEffCmdProtein.setStoreAlignments(storeAlignments);
snpEffCmdProtein.setCheckNumOk(checkNumOk);
snpEffCmdProtein.setProteinByTrId(proteinByTrId);
+ if( maxErrorRate >= 0) snpEffCmdProtein.setMaxErrorRate(maxErrorRate);
okProtein = snpEffCmdProtein.run();
if (!okProtein) {
if (verbose) Log.info("\tProtein sequences comparison failed!");
@@ -256,6 +263,11 @@ public class SnpEffCmdBuild extends SnpEff {
regSortedByType = true;
break;
+ case "-maxerrorrate":
+ if ((i + 1) < args.length) maxErrorRate = Gpr.parseDoubleSafe(args[++i]);
+ else usage("Missing 'maxErrorPercentage' argument");
+ break;
+
default:
usage("Unknown option '" + arg + "'");
}
@@ -461,6 +473,7 @@ public class SnpEffCmdBuild extends SnpEff {
System.err.println("\t-refseq : Use RefSeq table from UCSC.");
System.err.println("\nDatabase build options:");
System.err.println("\t-cellType <type> : Only build regulation tracks for cellType <type>.");
+ System.err.println("\t-maxErrorRate <num> : Maximum allowed error rate (number between 0.0 and 1.0). Default: 0.05");
System.err.println("\t-noCheckCds : Skip CDS sequences check.");
System.err.println("\t-noCheckProtein : Skip Protein sequences check.");
System.err.println("\t-noStoreSeqs : Do not store sequence in binary files. Default: " + !storeSequences);
=====================================
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdCds.java
=====================================
@@ -25,12 +25,12 @@ import java.util.List;
public class SnpEffCmdCds extends SnpEff {
public static boolean onlyOneError = false; // This is used in some test-cases
- public static double MAX_ERROR_PERCENTAGE = 0.05; // Maximum allowed error is 5% (otherwise test fails)
+ public static double MAX_ERROR_RATE = 0.05; // Maximum allowed error is 5% (otherwise test fails)
public static int MAX_ALIGN_LENGTH = 33000;
boolean storeAlignments; // Store alignments (used for some test cases)
boolean checkNumOk = true; // Require transcripts to be checked (more than zero)
- double maxErrorPercentage = MAX_ERROR_PERCENTAGE; // Maximum allowed error
+ double maxErrorRate = MAX_ERROR_RATE; // Maximum allowed error
int totalErrors = 0;
int totalOk = 0;
int totalWarnings = 0;
@@ -360,7 +360,7 @@ public class SnpEffCmdCds extends SnpEff {
var errorRate = cdsCompare();
if (verbose) Log.info("done");
- return errorRate <= maxErrorPercentage;
+ return errorRate <= maxErrorRate;
}
/**
@@ -394,6 +394,8 @@ public class SnpEffCmdCds extends SnpEff {
this.checkNumOk = checkNumOk;
}
+ public void setMaxErrorRate(double maxErrorRate) { this.maxErrorRate = maxErrorRate; }
+
public void setStoreAlignments(boolean storeAlignments) {
this.storeAlignments = storeAlignments;
}
=====================================
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdDatabases.java
=====================================
@@ -183,7 +183,6 @@ public class SnpEffCmdDatabases extends SnpEff {
// Show
System.out.println(String.format("%-60s\t%-60s\t%-10s\t%-30s\t%s", genomeVer, name, status, bundle, url));
- System.out.println(String.format("URL:\t%s", url));
}
}
=====================================
src/main/java/org/snpeff/snpEffect/commandLine/SnpEffCmdProtein.java
=====================================
@@ -25,7 +25,6 @@ import org.snpeff.snpEffect.factory.SnpEffPredictorFactoryEmbl;
import org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank;
import org.snpeff.util.Gpr;
import org.snpeff.util.Log;
-import org.snpeff.util.Timer;
/**
* Command line: Read protein sequences from a file and compare them to the ones calculated from our data structures
@@ -609,6 +608,8 @@ public class SnpEffCmdProtein extends SnpEff {
this.proteinByTrId = proteinByTrId;
}
+ public void setMaxErrorRate(double maxErrorRate) { this.maxErrorRate = maxErrorRate; }
+
public void setStoreAlignments(boolean storeAlignments) {
this.storeAlignments = storeAlignments;
}
=====================================
test_04_TestCasesEff.csv
=====================================
@@ -3,8 +3,8 @@
Name , Value
Genome , testHg3770Chr22
-Date , 2022-01-21 06:06
-SnpEff_version , SnpEff 5.1 (build 2022-01-18 17:09), by Pablo Cingolani
+Date , 2022-04-19 11:10
+SnpEff_version , SnpEff 5.1c (build 2022-04-19 10:57), by Pablo Cingolani
Command_line_arguments , SnpEff -csvStats test_04_TestCasesEff.csv testHg3770Chr22 tests/integration/eff/eff_sort.vcf
Warnings , 1096
Number_of_lines_in_input_file, 1205
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/3a21e7f88559157ed83b022daf37e891c39046d2
--
View it on GitLab: https://salsa.debian.org/med-team/snpeff/-/commit/3a21e7f88559157ed83b022daf37e891c39046d2
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