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])