Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
30
stars
4
forks
source link
Add check for non-unique genes, which causes overlap broadcast error #147
Users would experience a cryptic error during the overlap calculation stage. Error would say that operands could not be broadcast together due to incorrect shape. This error would show up if users did not properly quality-control their data and duplicate gene names were present. Duplicate gene names would cause instances of GeneDatum to have more than 1 start or stop value. Having more than 1 start or stop value would break the overlap calculation function.
Fix:
Add a check to the reading of preprocessed data. This check is at the pandas dataframe stage, before things are wrapped as GeneData or GeneDatum. The check raises an error if an index (a gene name) is non-unique.
Addresses #124
Problem:
Users would experience a cryptic error during the overlap calculation stage. Error would say that operands could not be broadcast together due to incorrect shape. This error would show up if users did not properly quality-control their data and duplicate gene names were present. Duplicate gene names would cause instances of
GeneDatumto have more than 1 start or stop value. Having more than 1 start or stop value would break the overlap calculation function.Fix:
Add a check to the reading of preprocessed data. This check is at the pandas dataframe stage, before things are wrapped as
GeneDataorGeneDatum. The check raises an error if an index (a gene name) is non-unique.