Annotation Script: annotateOthers

Overview

The annotateOthers script is designed to read information from a TSV file containing details about contigs, their positions, and coverages. A coverage value of zero is assigned to regions without any matching. The script identifies empty intersections (zero coverage) and annotates them as "others."

Usage

1. Input Data: Prepare a TSV genome coverage file with information about contigs, positions, and coverages.

2. Run the Script:

   python annotateOthers.py -i input_file.tsv -o output_file.tsv -f [tsv or bed6]
   

Options

• Specify the input TSV file using the -i flag.
• Specify the output name with the -o flag.
• The script also supports saving in BED9 format using the -f bed9 flag or tsv, default format ("tsv") if none is provided.
  • -f: Specify the output format (default is TSV, supports 'tsv' or 'bed9').

Dependencies

• Python 3.9.7
• pandas (for data manipulation)