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Fix bug that resulted in the TSL getting incorrectly evaluated when determining the best peptide #1036

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merged 5 commits into from
Nov 1, 2023
Merged

Fix bug that resulted in the TSL getting incorrectly evaluated when determining the best peptide #1036

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1307ab0
Update reference_matches file columns for pVACfuse and pVACbind
susannasiebert Aug 9, 2023
3317d2c
Merge remote-tracking branch 'origin/hotfix'
susannasiebert Aug 9, 2023
c78667b
Merge remote-tracking branch 'origin/hotfix'
susannasiebert Sep 8, 2023
60dcec2
Merge remote-tracking branch 'origin/hotfix'
susannasiebert Sep 26, 2023
a9b7f38
Fix bug that resulted in the TSL getting incorrectly evaluated when d…
susannasiebert Oct 31, 2023
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16 changes: 3 additions & 13 deletions docs/pvacbind/output_files.rst
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Expand Up @@ -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
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16 changes: 3 additions & 13 deletions docs/pvacfuse/output_files.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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2 changes: 1 addition & 1 deletion pvactools/lib/aggregate_all_epitopes.py
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Expand Up @@ -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
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