Now possible to add allele txt file in local folder

nf-core · Aug 31, 2023 · 89259c6 · 89259c6
1 parent 71e843b
commit 89259c6
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Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/bin/check_requested_models.py b/bin/check_requested_models.py
@@ -77,6 +77,8 @@ def __main__():
     # get the alleles
     if args.alleles.startswith("http"):
         alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").splitlines()]
+    elif args.alleles.endswith(".txt"):
+        alleles = [Allele(a) for a in open(args.alleles, "r").read().splitlines()]
     else:
         alleles = [Allele(a) for a in args.alleles.split(";")]
 

diff --git a/bin/epaa.py b/bin/epaa.py
@@ -1338,10 +1338,11 @@ def __main__():
     # get the alleles
     if args.alleles.startswith("http"):
         alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").splitlines()]
+    elif args.alleles.endswith(".txt"):
+        alleles = [Allele(a) for a in open(args.alleles, "r").read().splitlines()]
     else:
         alleles = [Allele(a) for a in args.alleles.split(";")]
 
-    print("alleles nach sache: ", alleles)
     # initialize MartsAdapter, GRCh37 or GRCh38 based
     ma = MartsAdapter(biomart=references[args.reference])