Systematic Mutations

Common Patterns

# Enumerate all single-position substitutions
echo ATGAAACCCGGGTTTTAG | systematic-mutations

# Preserve a second-column pattern label
echo 'ATG tag1' | systematic-mutations

# Expand ambiguous input first, then enumerate mutations
echo RCCGGY | disambiguate-nucleotides | systematic-mutations

Recommended Workflow

1. Feed one sequence per line on stdin, optionally followed by one extra whitespace-delimited label/pattern.
2. Normalize ambiguous bases upstream if you need explicit A/C/G/T inputs before mutation expansion.
3. Pipe the output directly into downstream text filters, because this tool does not create files by itself.
4. Deduplicate or rank the resulting variant strings downstream only if you need more than the built-in case-insensitive uniqueness pass.

Guardrails

• This script ignores command-line flags. Local testing showed systematic-mutations -h is silent with no stdin and behaves exactly like the normal mutator when stdin is present.
• Input is read from stdin only; the first whitespace-delimited token is the sequence and the second token, if present, is preserved as :<pattern>. Additional columns are ignored.
• The original sequence can reappear in the output because the substitution loop also tries the existing base at each position before the final sort -f | uniq -i.
• The script depends on transmute -replace; if transmute is missing from PATH, mutation generation fails.