From f3df8a8196f4ab7510ef7db864ef28d37bd56141 Mon Sep 17 00:00:00 2001 From: Clarke Date: Mon, 9 Oct 2023 17:07:46 +0200 Subject: [PATCH 1/3] bug fix --- deeprvat/annotations/annotations.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/deeprvat/annotations/annotations.py b/deeprvat/annotations/annotations.py index 39ffdfb9..766ce98f 100644 --- a/deeprvat/annotations/annotations.py +++ b/deeprvat/annotations/annotations.py @@ -480,8 +480,8 @@ def deepripe_score_variant_onlyseq_all( pred = model.predict_on_batch(cropped_seqs) wild_indices = tf.range(pred.shape[0], delta=2) mut_indices = tf.range(1, pred.shape[0], delta=2) - pred_wild = pred[wild_indices] - pred_mut = pred[mut_indices] + pred_wild = pred[wild_indices, :] + pred_mut = pred[mut_indices, :] score = pred_mut - pred_wild avg_score += score predictions[choice] = avg_score / 4 From ae950cc51ab8afea3cfc9a09c430761f4590bf90 Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Wed, 11 Oct 2023 09:54:50 +0200 Subject: [PATCH 2/3] Update ensembl-vep version --- deeprvat/annotations/setup_annotation_workflow.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/deeprvat/annotations/setup_annotation_workflow.sh b/deeprvat/annotations/setup_annotation_workflow.sh index 08b80726..76ba0d13 100644 --- a/deeprvat/annotations/setup_annotation_workflow.sh +++ b/deeprvat/annotations/setup_annotation_workflow.sh @@ -9,7 +9,7 @@ echo "- vep" mkdir -p $REPO_DIR/ensembl-vep git clone https://github.com/Ensembl/ensembl-vep.git $REPO_DIR/ensembl-vep cd $REPO_DIR/ensembl-vep -git checkout release/109 +git checkout release/111 perl INSTALL.pl --AUTO acfp --ASSEMBLY GRCh38 --CACHEDIR $VEP_CACHEDIR --PLUGINS CADD, SpliceAI, PrimateAI --PLUGINSDIR $VEP_PLUGINDIR --species homo_sapiens cd ../.. From df20e1ba0c6347913393c06be614364d5d2d088c Mon Sep 17 00:00:00 2001 From: Magnus Wahlberg Date: Fri, 13 Oct 2023 10:21:26 +0200 Subject: [PATCH 3/3] Make use of modules optional --- pipelines/annotations.snakefile | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/pipelines/annotations.snakefile b/pipelines/annotations.snakefile index 48804cb6..85531f06 100644 --- a/pipelines/annotations.snakefile +++ b/pipelines/annotations.snakefile @@ -26,11 +26,12 @@ saved_deepripe_models_path = ( ) merge_nthreads = int(config.get("merge_nthreads") or 64) -# init modules -load_bfc = " ".join([config["bcftools_load_cmd"], "&&"]) -load_hts = " ".join([config["htslib_load_cmd"], "&&"]) -load_perl = " ".join([config["perl_load_cmd"], "&&"]) -load_vep = " ".join([config["vep_load_cmd"], "&&"]) +# If modules are used we load them here +load_bfc = " ".join([config["bcftools_load_cmd"], "&&" if config["bcftools_load_cmd"] else ""]) +load_hts = " ".join([config["htslib_load_cmd"], "&&" if config["htslib_load_cmd"] else ""]) +load_perl = " ".join([config["perl_load_cmd"], "&&" if config["perl_load_cmd"] else ""]) +load_vep = " ".join([config["vep_load_cmd"], "&&" if config["vep_load_cmd"] else ""]) + # init data path vcf_pattern = config["vcf_file_pattern"]