Merge pull request #1036 from griffithlab/best_peptide

Fix bug that resulted in the TSL getting incorrectly evaluated when determining the best peptide
griffithlab · Nov 1, 2023 · 6fc9a9a · 6fc9a9a
2 parents 2d2c7df + a9b7f38
commit 6fc9a9a
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Showing 3 changed files with 7 additions and 27 deletions.
diff --git a/docs/pvacbind/output_files.rst b/docs/pvacbind/output_files.rst
@@ -258,19 +258,9 @@ option is chosen.
    * - Column Name
      - Description (BLAST)
      - Description (reference fasta)
-   * - ``Chromosome``
-     - :cspan:`2` The chromosome of this variant
-   * - ``Start``
-     - :cspan:`2` The start position of this variant in the zero-based, half-open coordinate system
-   * - ``Stop``
-     - :cspan:`2` The stop position of this variant in the zero-based, half-open coordinate system
-   * - ``Reference``
-     - :cspan:`2` The reference allele
-   * - ``Variant``
-     - :cspan:`2` The alt allele
-   * - ``Transcript``
-     - :cspan:`2` The Ensembl ID of the affected transcript
-   * - ``MT Epitope Seq``
+   * - ``ID``
+     - :cspan:`2` A unique identifier for the variant
+   * - ``Epitope Seq``
      - :cspan:`2` The mutant peptide sequence for the epitope candidate
    * - ``Peptide``
      - The peptide sequence submitted to BLAST

diff --git a/docs/pvacfuse/output_files.rst b/docs/pvacfuse/output_files.rst
@@ -326,19 +326,9 @@ option is chosen.
    * - Column Name
      - Description (BLAST)
      - Description (reference fasta)
-   * - ``Chromosome``
-     - :cspan:`2` The chromosome of this variant
-   * - ``Start``
-     - :cspan:`2` The start position of this variant in the zero-based, half-open coordinate system
-   * - ``Stop``
-     - :cspan:`2` The stop position of this variant in the zero-based, half-open coordinate system
-   * - ``Reference``
-     - :cspan:`2` The reference allele
-   * - ``Variant``
-     - :cspan:`2` The alt allele
-   * - ``Transcript``
-     - :cspan:`2` The Ensembl ID of the affected transcript
-   * - ``MT Epitope Seq``
+   * - ``ID``
+     - :cspan:`2` A unique identifier for the fusion
+   * - ``Epitope Seq``
      - :cspan:`2` The mutant peptide sequence for the epitope candidate
    * - ``Peptide``
      - The peptide sequence submitted to BLAST

diff --git a/pvactools/lib/aggregate_all_epitopes.py b/pvactools/lib/aggregate_all_epitopes.py
@@ -334,7 +334,7 @@ def get_best_binder(self, df):
         #subset protein_coding dataframe to only include entries with a TSL < maximum_transcript_support_level
         tsl_df = biotype_df[biotype_df['Transcript Support Level'] != 'NA']
         tsl_df = tsl_df[tsl_df['Transcript Support Level'] != 'Not Supported']
-        tsl_df = tsl_df[tsl_df['Transcript Support Level'] < self.maximum_transcript_support_level]
+        tsl_df = tsl_df[tsl_df['Transcript Support Level'] <= self.maximum_transcript_support_level]
         #if this results in an empty dataframe, reset to previous dataframe
         if tsl_df.shape[0] == 0:
             tsl_df = biotype_df