Updated download/install helper scripts.

data/training/download_dependencies.sh

@@ -0,0 +1,97 @@
+#!/bin/bash
+
+# create additional folder in borzoi data folders
+mkdir -p "$BORZOI_HG38/assembly/ucsc"
+mkdir -p "$BORZOI_HG38/assembly/gnomad"
+mkdir -p "$BORZOI_HG38/mappability"
+mkdir -p "$BORZOI_HG38/blacklist"
+mkdir -p "$BORZOI_HG38/align"
+
+mkdir -p "$BORZOI_MM10/assembly/ucsc"
+mkdir -p "$BORZOI_MM10/mappability"
+mkdir -p "$BORZOI_MM10/blacklist"
+
+
+# download and uncompress auxiliary files required for Makefile (hg38)
+if [ -f "$BORZOI_HG38/assembly/ucsc/hg38_gaps.bed" ]; then
+  echo "hg38_gaps.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/hg38_gaps.bed.gz | gunzip -c > "$BORZOI_HG38/assembly/ucsc/hg38_gaps.bed"
+fi
+
+if [ -f "$BORZOI_HG38/mappability/umap_k36_t10_l32.bed" ]; then
+  echo "umap_k36_t10_l32.bed (hg38) already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/umap_k36_t10_l32_hg38.bed.gz | gunzip -c > "$BORZOI_HG38/mappability/umap_k36_t10_l32.bed"
+fi
+
+if [ -f "$BORZOI_HG38/blacklist/blacklist_hg38_all.bed" ]; then
+  echo "blacklist_hg38_all.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/blacklist_hg38_all.bed.gz | gunzip -c > "$BORZOI_HG38/blacklist/blacklist_hg38_all.bed"
+fi
+
+if [ -f "$BORZOI_HG38/align/hg38.mm10.syn.net.gz" ]; then
+  echo "Splice site annotation already exist."
+else
+  wget https://storage.googleapis.com/seqnn-share/helper/dependencies/hg38.mm10.syn.net.gz -O "$BORZOI_HG38/align/hg38.mm10.syn.net.gz"
+fi
+
+
+# download and uncompress auxiliary files required for Makefile (mm10)
+if [ -f "$BORZOI_MM10/assembly/ucsc/mm10_gaps.bed" ]; then
+  echo "mm10_gaps.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/mm10_gaps.bed.gz | gunzip -c > "$BORZOI_MM10/assembly/ucsc/mm10_gaps.bed"
+fi
+
+if [ -f "$BORZOI_MM10/mappability/umap_k36_t10_l32.bed" ]; then
+  echo "umap_k36_t10_l32.bed (mm10) already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/umap_k36_t10_l32_mm10.bed.gz | gunzip -c > "$BORZOI_MM10/mappability/umap_k36_t10_l32.bed"
+fi
+
+if [ -f "$BORZOI_MM10/blacklist/blacklist_mm10_all.bed" ]; then
+  echo "blacklist_mm10_all.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/blacklist_mm10_all.bed.gz | gunzip -c > "$BORZOI_MM10/blacklist/blacklist_mm10_all.bed"
+fi
+
+
+# download and uncompress pre-compiled umap bed files
+if [ -f "$BORZOI_DIR/examples/umap_human.bed" ]; then
+  echo "umap_human.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/umap_human.bed.gz | gunzip -c > "$BORZOI_DIR/examples/umap_human.bed"
+fi
+
+if [ -f "$BORZOI_DIR/examples/umap_mouse.bed" ]; then
+  echo "umap_mouse.bed already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/umap_mouse.bed.gz | gunzip -c > "$BORZOI_DIR/examples/umap_mouse.bed"
+fi
+
+
+# download and index hg38 ml genome
+if [ -f "$BORZOI_HG38/assembly/ucsc/hg38.ml.fa" ]; then
+  echo "hg38.ml.fa already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/hg38.ml.fa.gz | gunzip -c > "$BORZOI_HG38/assembly/ucsc/hg38.ml.fa"
+  idx_genome.py "$BORZOI_HG38/assembly/ucsc/hg38.ml.fa"
+fi
+
+# download and index hg38 ml genome (gnomad major alleles)
+if [ -f "$BORZOI_HG38/assembly/gnomad/hg38.ml.fa" ]; then
+  echo "hg38.ml.fa (gnomad) already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/hg38_gnomad.ml.fa.gz | gunzip -c > "$BORZOI_HG38/assembly/gnomad/hg38.ml.fa"
+  idx_genome.py "$BORZOI_HG38/assembly/gnomad/hg38.ml.fa"
+fi
+
+# download and index mm10 ml genome
+if [ -f "$BORZOI_MM10/assembly/ucsc/mm10.ml.fa" ]; then
+  echo "mm10.ml.fa already exists."
+else
+  wget -O - https://storage.googleapis.com/seqnn-share/helper/dependencies/mm10.ml.fa.gz | gunzip -c > "$BORZOI_MM10/assembly/ucsc/mm10.ml.fa"
+  idx_genome.py "$BORZOI_MM10/assembly/ucsc/mm10.ml.fa"
+fi

model/train.sh

@@ -1,3 +1,3 @@
 #!/bin/sh
 
-westminster_train_folds.py -e borzoi_py310 --f_list 3 -c 4 --identical_crosses -q rtx4090 --rc -o saved_models params.json data/hg38 data/mm10
+westminster_train_folds.py -e borzoi_py310 --f_list 3 -c 4 --identical_crosses -q rtx4090 -o saved_models params.json data/hg38 data/mm10