windowmasker-2-2-22-adapter-py

name	windowmasker-2-2-22-adapter-py
description	Use when adapting or converting WindowMasker output files for compatibility with different BLAST pipeline versions or formats.
disable-model-invocation	true
user-invocable	true

windowmasker-2-2-22-adapter-py

Quick Start

• Command: windowmasker_2.2.22_adapter.py [--print-only] /path/to/windowmasker <old-style-options>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/windowmasker_2.2.22_adapter.py
• Full reference: See references/help.md

When To Use This Tool

• Translate historical WindowMasker 2.2.22-era command lines into the newer option style.
• Preserve old pipeline invocations while moving to a newer windowmasker binary.
• Preview the translated command with --print-only before executing it.
• Handle old mask, -mk_counts true, and -convert true style invocations without manually rewriting every option.

Common Patterns

# 1) Print the translated command without running it
windowmasker_2.2.22_adapter.py \
  --print-only \
  /home/vimalinx/miniforge3/envs/bio/bin/windowmasker \
  -mk_counts true \
  -in genome.fa \
  -out counts.obinary

# 2) Translate and execute an old masking command
windowmasker_2.2.22_adapter.py \
  /home/vimalinx/miniforge3/envs/bio/bin/windowmasker \
  -ustat counts.obinary \
  -in genome.fa \
  -out intervals.txt \
  -outfmt interval

# 3) Translate an old convert-mode command
windowmasker_2.2.22_adapter.py \
  --print-only \
  /home/vimalinx/miniforge3/envs/bio/bin/windowmasker \
  -convert true \
  -in wm.out \
  -out converted.out

Recommended Workflow

1. Treat this as a migration helper for old WindowMasker command lines, not as a primary masking tool.
2. Start with --print-only and compare the translated command to the current windowmasker -help output.
3. Keep the actual windowmasker executable path explicit; the adapter passes it through unchanged.
4. Once translation looks correct, run the real windowmasker command or let the adapter execute it for you.

Guardrails

• This script uses Python 2 syntax; in the current workspace it fails under Python 3, and python2 is not available on PATH.
• The first non-flag argument must be the target windowmasker executable; the adapter does not discover it for you.
• --print-only is the safe default because the adapter will otherwise execute the translated command via os.system.
• The adapter silently drops or preserves old options based on mode (mask, mk_counts, or convert), so always inspect the translated command before trusting it.
• If you are already on a modern pipeline, prefer calling windowmasker directly instead of introducing this compatibility shim.