Merge pull request #211 from alina-bauer/dev

Allele data can also be used via internet link in sample sheet

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 +75,12 @@ 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()]
+    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(";")]
 
     peptide_lengths = []
     if args.peptides:

bin/check_samplesheet.py

@@ -274,7 +274,7 @@ def check_samplesheet(file_in, file_out):
         out_dir = os.path.dirname(file_out)
         make_dir(out_dir)
         with open(file_out, "w") as fout:
-            valid_header.append("file_type")
+            valid_header.append("inputtype")
             fout.write(",".join(valid_header) + "\n")
             for row in rows:
                 fout.write(",".join(row) + "\n")

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
@@ -1335,8 +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()]
+    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(";")]
 
     # initialize MartsAdapter, GRCh37 or GRCh38 based
     ma = MartsAdapter(biomart=references[args.reference])