From 84efa733132719b7be93bb5661a025f80b739499 Mon Sep 17 00:00:00 2001 From: Xiang Li Date: Wed, 28 Aug 2024 14:04:26 -0400 Subject: [PATCH] Revert "Mutation assessor v4" --- .../export/annotation_version.txt | 2 +- .../input/annotation_version.txt | 8 ----- .../export/annotation_version.txt | 1 - scripts/import_mongo.sh | 34 +++++++++---------- 4 files changed, 17 insertions(+), 28 deletions(-) delete mode 100644 data/grch38_ensembl92/input/annotation_version.txt diff --git a/data/grch37_ensembl92/export/annotation_version.txt b/data/grch37_ensembl92/export/annotation_version.txt index 8ae921a..afd9bf7 100644 --- a/data/grch37_ensembl92/export/annotation_version.txt +++ b/data/grch37_ensembl92/export/annotation_version.txt @@ -4,6 +4,6 @@ HGNC 2023-10 mirrored hgnc The resource for approved human gene nomenclature. Ge Cancer Hotspots v2 mirrored cancer_hotspots A resource for statistically significant mutations in cancer https://www.cancerhotspots.org 3D Hotspots v2 mirrored 3d_hotspots A resource for statistically significant mutations clustering in 3d protein structures in cancer https://www.3dhotspots.org/ reVUE https://github.com/knowledgesystems/reVUE-data/blob/main/VUEs.json mirrored revue A Repository for Variants with Unexpected Effects (VUE) in Cancer https://www.cancerrevue.org/ -Mutation Assessor v4 mirrored mutation_assessor Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. http://mutationassessor.org/r3/ +Mutation Assessor v3 mirrored mutation_assessor Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. http://mutationassessor.org/r3/ My Variant Info Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html external my_variant_info MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources. https://myvariant.info ClinVar 20230722 mirrored clinvar ClinVar aggregates information about genomic variation and its relationship to human health. https://www.ncbi.nlm.nih.gov/clinvar/ diff --git a/data/grch38_ensembl92/input/annotation_version.txt b/data/grch38_ensembl92/input/annotation_version.txt deleted file mode 100644 index d8895a0..0000000 --- a/data/grch38_ensembl92/input/annotation_version.txt +++ /dev/null @@ -1,8 +0,0 @@ -name version type id description url -VEP grch38 mirrored vep VEP determines the effect of your variants(SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. https://useast.ensembl.org/info/docs/tools/vep/index.html -HGNC 2023-10 mirrored hgnc The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/ -Cancer Hotspots v2 mirrored cancer_hotspots A resource for statistically significant mutations in cancer https://www.cancerhotspots.org -3D Hotspots v2 mirrored 3d_hotspots A resource for statistically significant mutations clustering in 3d protein structures in cancer https://www.3dhotspots.org/ -Mutation Assessor v4 mirrored mutation_assessor Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. http://mutationassessor.org/r3/ -My Variant Info Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html external my_variant_info MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources. https://myvariant.info -ClinVar 20230722 mirrored clinvar ClinVar aggregates information about genomic variation and its relationship to human health. https://www.ncbi.nlm.nih.gov/clinvar/ diff --git a/data/grch38_ensembl95/export/annotation_version.txt b/data/grch38_ensembl95/export/annotation_version.txt index d8895a0..1d418cc 100644 --- a/data/grch38_ensembl95/export/annotation_version.txt +++ b/data/grch38_ensembl95/export/annotation_version.txt @@ -3,6 +3,5 @@ VEP grch38 mirrored vep VEP determines the effect of your variants(SNPs, inserti HGNC 2023-10 mirrored hgnc The resource for approved human gene nomenclature. Genome Nexus uses HGNC gene symbols in annotation http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/archive/monthly/tsv/ Cancer Hotspots v2 mirrored cancer_hotspots A resource for statistically significant mutations in cancer https://www.cancerhotspots.org 3D Hotspots v2 mirrored 3d_hotspots A resource for statistically significant mutations clustering in 3d protein structures in cancer https://www.3dhotspots.org/ -Mutation Assessor v4 mirrored mutation_assessor Mutation Assessor predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. http://mutationassessor.org/r3/ My Variant Info Includes many annotation sources, see https://docs.myvariant.info/en/latest/doc/data.html external my_variant_info MyVariant.info provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources. https://myvariant.info ClinVar 20230722 mirrored clinvar ClinVar aggregates information about genomic variation and its relationship to human health. https://www.ncbi.nlm.nih.gov/clinvar/ diff --git a/scripts/import_mongo.sh b/scripts/import_mongo.sh index 2957f74..c15f5de 100755 --- a/scripts/import_mongo.sh +++ b/scripts/import_mongo.sh @@ -52,24 +52,22 @@ elif [[ ${REF_ENSEMBL_VERSION} == *"grch38"* ]]; then fi # import mutation assessor -echo "Downloading Mutation assessor data" -# Data source: https://drive.google.com/file/d/1V6r65xJFF5fJ7b9JHwqkvCe8wWDrIBhd/view. -# The copy is stored in S3 bucket: ttps://genome-nexus-static-data.s3.amazonaws.com/mutationassessor4_for_genome_nexus.tsv.xz -curl https://genome-nexus-static-data.s3.amazonaws.com/mutationassessor4_for_genome_nexus.tsv.xz -o ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.xz -echo "Download completed." - -echo "Extracting Mutation assessor data" -unxz -k ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.xz - -echo "Transforming Mutation assessor data" -sed -i '' 's/uniprotId\tSV\thgvspShort\tF_score\tF_impact\tMSA\tMAV/uniprotId\tsv\thgvspShort\tf_score\tf_impact\tmsa\tmav/' ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv -awk -F'\t' 'BEGIN{OFS="\t"} NR==1{print "_id",$0; next} {print $1","$3,$0}' ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv > processed_mutaiton_assessor_tsv_file.tsv -rm ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv.xz -rm ${DIR}/../data/common_input/mutationassessor4_for_genome_nexus.tsv - -echo "Importing Mutation assessor data" -import mutation_assessor.annotation processed_mutaiton_assessor_tsv_file.tsv "--type tsv --headerline" -rm processed_mutaiton_assessor_tsv_file.tsv +if [[ ${REF_ENSEMBL_VERSION} == *"grch37"* && ${MUTATIONASSESSOR} == true ]]; then + echo "Downloading Mutation assessor data" + + curl http://mutationassessor.org/r3/MA_scores_rel3_hg19_full.tar.gz -o ${DIR}/../data/common_input/MA_scores_rel3_hg19_full.tar.gz + + echo "Extracting Mutation assessor data" + tar -xvf ${DIR}/../data/common_input/MA_scores_rel3_hg19_full.tar.gz + rm ${DIR}/../data/common_input/MA_scores_rel3_hg19_full.tar.gz + + echo "Transforming Mutation assessor data" + sed -i -e 's/"Mutation","RefGenome variant","Gene","Uniprot","Info","Uniprot variant","Func. Impact","FI score"/_id,rgaa,gene,uprot,info,var,F_impact,F_score/g' MA_scores_rel3_hg19_full/MA_scores_rel3_hg19_chr* + sed -i -e 's/hg19,//g' MA_scores_rel3_hg19_full/MA_scores_rel3_hg19_chr* + + echo "Importing Mutation assessor data" + for filename in MA_scores_rel3_hg19_full/*.csv; do import mutation_assessor.annotation $filename '--type csv --headerline' && rm $filename; done +fi # import annotation sources version import version ${DIR}/../data/${REF_ENSEMBL_VERSION}/export/annotation_version.txt '--drop --type tsv --headerline' \ No newline at end of file