legacy-blast-pl

name	legacy-blast-pl
description	Use when converting NCBI C toolkit BLAST command lines to NCBI C++ toolkit equivalents.
disable-model-invocation	true
user-invocable	true

legacy-blast-pl

Quick Start

• Command: legacy_blast.pl <legacy_program> <legacy_args> [--print_only] [--path /path/to/blast/bin]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/legacy_blast.pl
• Full reference: See references/help.md

When To Use This Tool

• Translate old NCBI C toolkit BLAST command lines into BLAST+ / C++ toolkit equivalents.
• Preserve historical reproducibility when old pipeline logs mention blastall, formatdb, fastacmd, or related legacy programs.
• Preview modern replacement commands with --print_only before executing them.
• Use it as a migration helper, not as a routine front end for new BLAST workflows.

Common Patterns

# 1) Preview a blastall-to-BLAST+ translation
legacy_blast.pl \
  blastall -p blastp -i query.fa -d nr -e 1e-5 \
  --print_only \
  --path /home/vimalinx/miniforge3/envs/bio/bin

# 2) Preview a formatdb migration
legacy_blast.pl \
  formatdb -i proteins.fa -p T \
  --print_only \
  --path /home/vimalinx/miniforge3/envs/bio/bin

# 3) Execute the translated command directly
legacy_blast.pl \
  fastacmd -d nr -s NP_414543 \
  --path /home/vimalinx/miniforge3/envs/bio/bin

Recommended Workflow

1. Identify the original legacy command exactly as it appeared in historical documentation or scripts.
2. Use --print_only first and review the translated BLAST+ command for semantic drift.
3. Point --path at the BLAST+ binaries you actually want to use on this machine.
4. Replace the old command permanently once the translated command has been validated on a small example.

Guardrails

• Script-level options such as --print_only and --path must use double dashes and appear at the end of the legacy command line.
• The default binary path is /usr/bin, which is usually wrong in this workspace; prefer --path /home/vimalinx/miniforge3/envs/bio/bin.
• Supported legacy applications are limited to the ones hard-coded in the script, including blastall, megablast, blastpgp, bl2seq, rpsblast, fastacmd, formatdb, and seedtop.
• Translation is not guaranteed to be biologically identical; inspect the generated command, especially filtering, scoring, and formatting options.
• --version only works as the first and only argument to the script.