From ba86ddb6e85dfe9f2cc66d00bfd4ec4cefe22a66 Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Fri, 26 Mar 2021 20:26:02 +0000 Subject: [PATCH] Fixed the previous commit --- Mikado/_transcripts/transcript_base.py | 3 ++- Mikado/parsers/bed12.py | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/Mikado/_transcripts/transcript_base.py b/Mikado/_transcripts/transcript_base.py index 1eb29869..c0dd14b1 100644 --- 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 index 7c617bb1..9886d6f1 100644 --- 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