Add option to enter alleles as internet link to samplesheet

nf-core · Aug 31, 2023 · e6e441e · e6e441e
1 parent 50812f9
commit e6e441e
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/bin/check_requested_models.py b/bin/check_requested_models.py
@@ -6,6 +6,7 @@
 import csv
 import argparse
 import logging
+import urllib.request
 
 from epytope.Core.Allele import Allele
 from epytope.Core.Peptide import Peptide
@@ -74,7 +75,10 @@ def __main__():
         }
 
     # get the alleles
-    alleles = [Allele(a) for a in args.alleles.split(";")]
+    if args.alleles.startswith("http"):
+        alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").splitlines()]
+    else:
+        alleles = [Allele(a) for a in args.alleles.split(";")]
 
     peptide_lengths = []
     if args.peptides:

diff --git a/bin/epaa.py b/bin/epaa.py
@@ -15,6 +15,7 @@
 import epytope.Core.Generator as generator
 import math
 import json
+import urllib.request
 
 from epytope.IO.MartsAdapter import MartsAdapter
 from epytope.Core.Variant import Variant, VariationType, MutationSyntax
@@ -1335,9 +1336,12 @@ def __main__():
         )
 
     # get the alleles
-    # alleles = FileReader.read_lines(args.alleles, in_type=Allele)
-    alleles = [Allele(a) for a in args.alleles.split(";")]
+    if args.alleles.startswith("http"):
+        alleles = [Allele(a) for a in urllib.request.urlopen(args.alleles).read().decode("utf-8").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])