feat: add DECIPHER HI predictions v3 (#63)

Author: holtgrewe

Snakefile

@@ -89,6 +89,7 @@ rule all:
         f"work/download/genes/rcnv/2022/Collins_rCNV_2022.dosage_sensitivity_scores.tsv.gz",
         f"work/download/genes/orphapacket/{DV.orphapacket}/orphapacket.tar.gz",
         f"work/genes/dbnsfp/{DV.dbnsfp}/genes.tsv.gz",
+        "work/genes/decipher/v3/decipher_hi_prediction.tsv.gz",
         f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv",
         f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv",
         f"work/genes/entrez/{DV.today}/gene_info.jsonl",
@@ -329,6 +330,7 @@ include: "rules/work/misc/hpo.smk"
 # Gene-related rules.
 include: "rules/work/genes/dbnsfp.smk"
 include: "rules/work/genes/clingen.smk"
+include: "rules/work/genes/decipher.smk"
 include: "rules/work/genes/ensembl.smk"
 include: "rules/work/genes/gnomad.smk"
 include: "rules/work/genes/gtex.smk"

download_urls.yml

@@ -1,3 +1,5 @@
+- url: https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz
+
 - url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh37.tsv
 - url: ftp://ftp.clinicalgenome.org/ClinGen_region_curation_list_GRCh38.tsv
 

excerpt-data/86ffcde07ca5f388/HI_Predictions_Version3.bed.gz

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f2d2ed0ba3247c444a0f55a0659d16b253f6030108e3497785505d11dea72838
+size 3072

excerpt-data/86ffcde07ca5f388/url.txt

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5daa1c09650953bb18b68be21872a95a222b60e1619b3959a1cb8d443e40a055
+size 80

rules/work/genes/decipher.smk

@@ -0,0 +1,57 @@
+## Rules related to DECIPHER gene information.
+
+
+rule genes_decipher_hi_download:  # -- download DECIPHER HI predictions
+    output:
+        bed="work/download/genes/decipher/v3/HI_Predictions_Version3.bed.gz",
+        bed_md5="work/download/genes/decipher/v3/HI_Predictions_Version3.bed.gz.md5",
+    shell:
+        r"""
+        wget --no-check-certificate \
+            -O {output.bed} \
+            https://www.deciphergenomics.org/files/downloads/HI_Predictions_Version3.bed.gz
+
+        md5sum {output.bed} > {output.bed_md5}
+        """
+
+
+rule genes_decipher_hi_convert:  # -- convert DECIPHER HI predictions to TSV
+    input:
+        hgnc=f"output/full/mehari/genes-xlink-{DV.today}/genes-xlink.tsv",
+        bed="work/download/genes/decipher/v3/HI_Predictions_Version3.bed.gz",
+    output:
+        tsv="work/genes/decipher/v3/decipher_hi_prediction.tsv.gz",
+        tsv_md5="work/genes/decipher/v3/decipher_hi_prediction.tsv.gz.md5",
+    shell:
+        r"""
+        set -x
+
+        export TMPDIR=$(mktemp -d)
+        trap "rm -rf $TMPDIR" EXIT
+
+        echo -e "gene_symbol\tp_hi\thi_index" > $TMPDIR/tmp.tsv
+
+        zcat {input.bed} \
+        | tail -n +2 \
+        | cut -f 4 \
+        | tr '|' '\t' \
+        | sed -e 's/%$//g' \
+        >> $TMPDIR/tmp.tsv
+
+        qsv join \
+            gene_symbol {input.hgnc} \
+            gene_symbol $TMPDIR/tmp.tsv \
+        > $TMPDIR/tmp2.tsv
+
+        ( \
+            echo -e "hgnc_id\thgnc_symbol\tp_hi\thi_index"; \
+            tail -n +2 $TMPDIR/tmp2.tsv \
+            | tr ',' '\t' \
+            | cut -f 1,5-7 \
+            | LC_ALL=C sort \
+        ) \
+        | gzip -c \
+        > {output.tsv}
+
+        md5sum {output.tsv} > {output.tsv_md5}
+        """