feat: allow providing clinvar version (#17)

bihealth · Jun 21, 2023 · dd80f2d · dd80f2d
1 parent 6e7ac01
commit dd80f2d
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Showing 2 changed files with 8 additions and 13 deletions.
diff --git a/clinvar_tsv/Snakefile b/clinvar_tsv/Snakefile
@@ -1,5 +1,9 @@
+import os
 import os.path
 
+#: ClinVar version to download.
+CLINVAR_VERSION = os.environ.get("CLINVAR_VERSION")
+
 #: Path to b37/b38 FASTA file
 REF = {
     'b37': config.get('b37_path', '/dev/null'),
@@ -18,27 +22,17 @@ rule default:
 
 
 rule download_xml:
-    output: "downloads/ClinVarFullRelease_00-latest.xml.gz"
-    shell:
-        r"""
-        wget -c -N -O {output} ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/ClinVarFullRelease_00-latest.xml.gz \
-        2> {output}.log
-        """
-
-
-rule download_txt:
-    output: "downloads/variant_summary.txt.gz"
+    output: "downloads/ClinVarFullRelease_{clinvar_version}.xml.gz"
     shell:
         r"""
-        wget -c -N -O {output} ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz \
+        wget -c -N -O {output} https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/weekly_release/ClinVarFullRelease_{wildcards.clinvar_version}.xml.gz \
         2> {output}.log
         """
 
 
 rule parse_clinvar:
     input:
-        release_xml="downloads/ClinVarFullRelease_00-latest.xml.gz",
-        summary="downloads/variant_summary.txt.gz",
+        release_xml=f"downloads/ClinVarFullRelease_{CLINVAR_VERSION}.xml.gz"
     output:
         b37_small="parsed/clinvar_table_raw.b37.tsv",
         b37_sv="parsed/clinvar_sv.b37.tsv",

diff --git a/clinvar_tsv/__main__.py b/clinvar_tsv/__main__.py
@@ -182,6 +182,7 @@ def main(argv=None):
     parser_merge_tsvs.set_defaults(func=run_merge_tsvs)
 
     args = parser.parse_args(argv)
+    os.environ["CLINVAR_VERSION"] = args.clinvar_version
     return run(args)