Merge pull request #462 from griffithlab/hotfix_pvacbind

Update all output parsers to handle IEDB files with Warning line

.travis.yml

@@ -22,6 +22,8 @@ install:
   - pip install tornado==5.0.2
   - pip install jsonschema==2.6.0
   - pip install mhcnuggets==2.2
+  - pip install tensorflow==1.14.0
+  - pip install keras==2.2.5
 services:
   - postgresql
 script:

lib/output_parser.py

@@ -551,6 +551,8 @@ def parse_iedb_file(self, tsv_entries):
                 iedb_tsv_reader = csv.DictReader(reader, delimiter='\t')
                 (sample, method, remainder) = os.path.basename(input_iedb_file).split(".", 2)
                 for line in iedb_tsv_reader:
+                    if "Warning: Potential DNA sequence(s)" in line['allele']:
+                        continue
                     protein_label  = int(line['seq_num'])
                     if 'core_peptide' in line:
                         position   = str(int(line['start']) - line['peptide'].find(line['core_peptide']))
@@ -596,6 +598,8 @@ def parse_iedb_file(self):
                 iedb_tsv_reader = csv.DictReader(reader, delimiter='\t')
                 (sample, method, remainder) = os.path.basename(input_iedb_file).split(".", 2)
                 for line in iedb_tsv_reader:
+                    if "Warning: Potential DNA sequence(s)" in line['allele']:
+                        continue
                     protein_label  = int(line['seq_num'])
                     if 'core_peptide' in line:
                         position   = str(int(line['start']) - line['peptide'].find(line['core_peptide']))