Centralize "Split" File Path Generation

pvacseq/lib/__init__.py

@@ -3,17 +3,22 @@
     "call_iedb",
     "combine_parsed_outputs",
     "config_files",
-    "convert_vcf",
+    "input_file_converter",
     "coverage_filter",
     "download_example_data",
-    "generate_fasta",
+    "fasta_generator",
     "generate_protein_fasta",
     "install_vep_plugin",
     "main",
-    "parse_output",
+    "output_parser",
     "valid_alleles",
     'net_chop',
-    "netmhc_stab"
+    "netmhc_stab",
 ]
 
+import os
+import sys
+pvac_dir = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
+sys.path.append(pvac_dir)
+sys.path.append(os.path.join(pvac_dir, 'pvacseq'))
 from . import *

pvacseq/lib/call_iedb.py

@@ -1,12 +1,8 @@
 import sys
-from pathlib import Path # if you haven't already done so
-root = str(Path(__file__).resolve().parents[1])
-sys.path.append(root)
-
+import os
 import argparse
 import requests
 import re
-import os
 from lib.prediction_class import *
 import time
 from subprocess import run, PIPE