fit variation file suffix

snakemake · Dec 12, 2019 · da9eab8 · da9eab8
1 parent 0a3d6e7
commit da9eab8
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/bio/reference/ensembl-variation/wrapper.py b/bio/reference/ensembl-variation/wrapper.py
@@ -14,14 +14,14 @@
 if type == "all":
     if species == "homo_sapiens":
         suffixes = [
-            "chr{}".format(chrom) for chrom in list(range(1, 23)) + ["X", "Y", "MT"]
+            "_chr{}".format(chrom) for chrom in list(range(1, 23)) + ["X", "Y", "MT"]
         ]
     else:
         suffixes = [""]
 elif type == "somatic":
-    suffixes = ["somatic"]
+    suffixes = ["_somatic"]
 elif type == "structural_variations":
-    suffixes = ["structural_variations"]
+    suffixes = ["_structural_variations"]
 else:
     raise ValueError(
         "Unsupported type {} (only all, somatic, structural_variations are allowed)".format(
@@ -30,7 +30,7 @@
     )
 
 urls = [
-    "ftp://ftp.ensembl.org/pub/release-{release}/variation/vcf/{species}/{species}_{suffix}.vcf.gz".format(
+    "ftp://ftp.ensembl.org/pub/release-{release}/variation/vcf/{species}/{species}{suffix}.vcf.gz".format(
         release=release, species=species, suffix=suffix
     )
     for suffix in suffixes