fix (splitFasta): made --variant-peptide optional

moPepGen/cli/split_fasta.py

@@ -39,7 +39,8 @@ def add_subparser_split_fasta(subparser:argparse._SubParsersAction):
         type=Path,
         help='File path to the variant peptide FASTA database file. Must be'
         f" generated by moPepGen callVariant. Valid formats: {FASTA_FILE_FORMAT}",
-        metavar='<file>'
+        metavar='<file>',
+        default=None
     )
     p.add_argument(
         '--noncoding-peptides',
@@ -54,7 +55,8 @@ def add_subparser_split_fasta(subparser:argparse._SubParsersAction):
         type=Path,
         help='File path to the alt translation peptide FASTA file. Must be'
         f"generated by moPepGen callAltTranslation. Valid formats: {FASTA_FILE_FORMAT}",
-        metavar='<file>'
+        metavar='<file>',
+        default=None
     )
     p.add_argument(
         '-o', '--output-prefix',
@@ -109,7 +111,13 @@ def split_fasta(args:argparse.Namespace) -> None:
         common.validate_file_format(
             file, GVF_FILE_FORMAT, check_readable=True
         )
-    for file in [args.variant_peptides, args.noncoding_peptides]:
+    peptide_fastas = [args.variant_peptides, args.noncoding_peptides, args.alt_translation_peptides]
+    if all(x is None for x in peptide_fastas):
+        raise ValueError(
+            "At least one of '--variant-peptide', '--noncoding-peptide' or"
+            "' --alt-translation-peptide' must be given. Please verify your command."
+        )
+    for file in peptide_fastas:
         if file is not None:
             common.validate_file_format(
                 file, FASTA_FILE_FORMAT, check_readable=True
@@ -155,10 +163,10 @@ def split_fasta(args:argparse.Namespace) -> None:
 
     splitter = PeptidePoolSplitter(order=source_order, group_map=group_map)
 
-    with open(args.variant_peptides, 'rt') as handle:
-        splitter.load_database(handle)
-
-    logger(f"Variant FASTA loaded: {args.variant_peptides}.")
+    if args.variant_peptides:
+        with open(args.variant_peptides, 'rt') as handle:
+            splitter.load_database(handle)
+        logger(f"Variant FASTA loaded: {args.variant_peptides}.")
 
     if args.noncoding_peptides:
         with open(args.noncoding_peptides, 'rt') as handle:

test/integration/test_split_fasta.py

@@ -210,3 +210,21 @@ def test_split_fasta_source_order_comb(self):
         ])
         args.max_source_groups = 2
         cli.split_fasta(args)
+
+    def test_split_fasta_noncoding_and_alttrans(self):
+        """ test splitFasta with only noncoding and alt trans peptides """
+        args = self.create_base_args()
+        args.gvf = [
+        ]
+        args.variant_peptides = None
+        args.noncoding_peptides = self.data_dir/'peptides/noncoding.fasta'
+        args.alt_translation_peptides = self.data_dir/'peptides/alt_translation.fasta'
+        args.annotation_gtf = self.data_dir/'annotation.gtf'
+        args.proteome_fasta = self.data_dir/'translate.fasta'
+        cli.split_fasta(args)
+        files = {str(file.name) for file in self.work_dir.glob('*')}
+        expected = {
+            'test_Noncoding.fasta', 'test_SECT.fasta',
+            'test_Remaining.fasta', 'test_CodonReassign.fasta'
+        }
+        self.assertEqual(files, expected)