Merge pull request #94 from genome-nexus/revert-92-mutation-assessor-v4

Revert "Mutation assessor v4"

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/

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/

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'