Fixed the previous commit

EI-CoreBioinformatics · Mar 26, 2021 · ba86ddb · ba86ddb
1 parent 182ae18
commit ba86ddb
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/Mikado/_transcripts/transcript_base.py b/Mikado/_transcripts/transcript_base.py
@@ -793,8 +793,9 @@ def get_internal_orf_beds(self) -> List[BED12]:
             row.block_sizes = [0]
             row = BED12(row, seq,
                         coding=False, transcriptomic=True, max_regression=0, start_adjustment=False,
+                        lenient=True,
                         table=self.codon_table)
-            if row.invalid is False:
+            if row.invalid is True:
                 raise AssertionError("\n".join([str(row), row.invalid_reason]))
             yield row
         else:

diff --git a/Mikado/parsers/bed12.py b/Mikado/parsers/bed12.py
@@ -668,7 +668,7 @@ def __check_validity(self, transcriptomic, fasta_index, sequence):
                               self.chrom, self.has_start_codon, self.has_stop_codon, not self.invalid)
 
             # Get only a proper multiple of three
-            if self.lenient is False:
+            if self.lenient is False and self.coding is True:
                 if self.strand != "-":
                     orf_sequence = sequence[
                                    (self.thick_start - 1 if not self.phase