pyEager 1.6.2

A simple package to read in eager results.

pyEager

A simple package to read in eager results.

Available functions

• compile_endogenous_table(): Creates a compiled table of endogenous DNA statistics from endorspy including all the information in the list of JSON file paths provided. Wraps parse_endorspy_json on all provided JSON paths.
  • parse_endorspy_json(): Read in the information in a single endorspy JSON file.
• compile_damage_table(): Creates a compiled table of select DamageProfiler and mapDamage2 results from the list of DamageProfiler JSON files and/or mapDamage2 result directories provided. Ths resulting dataframe includes the number of reads analysed as well as the damage in the first 2 bp of either end of DNA molecules for each sample.
  • collect_damageprofiler_results(): Collects the results from multiple damageprofiler JSON output files into a large dictionary containing all the results for each sample. This function wraps parse_damageprofiler_json across all provided JSON files.
    • parse_damageprofiler_json(): Read in the information in a single damageprofiler JSON output file.
  • collect_mapdamage_results(): Collects the results from multiple mapDamage2 result directories into a large dictionary containing all the results for each sample. This function wraps parse_mapdamage_results across all provided result directories.
    • parse_mapdamage_results(): Read in the information in a single mapDamage2 results directory. An additional parameter standardise_colnames can be used to standardise the column names of the resulting dataframe to match those generated by parse_damageprofiler_json.
• compile_snp_coverage_table(): Creates a compiled table of SNP coverage results from the list of JSON files provided. Wraps parse_snp_coverage_json across all provided JSON files
  • parse_snp_coverage_json(): Read in the information in a single SNP coverage JSON file.
• parse_sexdeterrmine_json(): Reads in the Sexdeterrmine output JSON into a dataframe.
• parse_nuclear_contamination_json(): Reads in the nuclear contamination output JSON into a dataframe.
• parse_eager_tsv(): Reads in the eager input TSV into a dataframe, with additional columns specifying what merging steps took place.
• infer_merged_bam_names(): Infer the names of eager output files based on the merging steps that took place.
• parse_general_stats_table(): Reads in the general stats table output of MultiQC into a dataframe.

Installation

Usage

License

MIT