abbr

Behavior:

• Abbreviates strain scientific names to unique short identifiers.
• Generates abbreviations for genus, species, and strain parts.
• Handles special cases like Candidatus and subspecies names.
• Ensures uniqueness of abbreviations across all input names.

Input:

• Accepts a TSV/CSV file or standard input.
• Each row should contain strain, species, and genus names in separate columns.
• Use --column to specify which columns contain these names (default: 1,2,3).
• Common column patterns:
  • 1,2,3 - strain in column 1, species in 2, genus in 3
  • 1,1,2 - no strain: strain and species both in column 1, genus in 2
  • 2,2,3 - don’t need strain part: strain and species in 2, genus in 3
  • 1,1,1 - only strain: all three in column 1

Output:

• Original line followed by a tab and the generated abbreviation.
• Abbreviation format:
  • Normal mode: Genus_Species_Strain (e.g., H_sapiens_sapiens)
  • Tight mode (--tight): GenusSpecies_Strain (e.g., Hsapiens_sapiens)
• Special handling:
  • Candidatus is abbreviated to C
  • Non-alphanumeric characters are replaced with underscores
  • Consecutive underscores are collapsed
  • Leading and trailing underscores are removed

Examples:

1. Basic usage with default columns echo -e 'Homo sapiens,Homo\nHomo erectus,Homo' | nwr abbr -s ',' -c "1,1,2"

2. Tight mode (no underscore between genus and species) echo -e 'Homo sapiens,Homo\nHomo erectus,Homo' | nwr abbr -s ',' -c "1,1,2" --tight

3. Clean subspecies names echo 'Legionella pneumophila subsp. pneumophila' | nwr abbr --shortsub

4. Process a file nwr abbr names.tsv -o abbreviated.tsv

5. Custom separator and columns nwr abbr data.csv -s ',' -c "1,2,3" -o output.tsv