transmute

name	transmute
description	Use when invoking the public `transmute` wrapper for format conversion, sequence editing, or shell-level helper modes that may be intercepted before dispatch to the platform binary.
disable-model-invocation	true
user-invocable	true

transmute

Public wrapper script for the NCBI transmute toolkit. Some modes are handled directly in shell, Perl, Python, or xmllint helpers, while the remaining arguments are passed through to the compiled platform-specific executable such as transmute.Linux.

Quick Start

• Command: transmute [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/transmute
• Platform backend here: transmute.Linux

When To Use This Tool

• Using the preferred public transmute entry point instead of calling the platform binary directly
• Running format-conversion or sequence-processing modes described in transmute -help
• Accessing shell-intercepted convenience modes such as -j2p, -x2p, -sort-by-length, or XML encode/decode helpers
• Building pipelines that should stay portable across platforms because the wrapper selects the correct compiled backend

Common Patterns

# Convert JSON to XML through the public wrapper
printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec

# Pretty-print JSON using the wrapper's python helper path
printf '{"a":1}\n' | transmute -j2p

# Wrapper-level line-length sort helper
printf 'bbb\na\ncc\n' | transmute -sort-by-length

Recommended Workflow

1. Start with transmute -help to choose the right mode.
2. Prefer the wrapper over transmute.Linux when you want portability or wrapper-only helper modes.
3. Feed data through stdin unless the selected mode explicitly documents file-based arguments.
4. If a mode behaves oddly, check whether it is one of the shell-intercepted paths before blaming the compiled backend.

Guardrails

• transmute -help and transmute -version both work here and report version 24.0.
• The wrapper intercepts several modes itself, including -encodeXML, -decodeXML, -plainXML, -x2p, -j2p, -x2j, -word-pairs, -sort-by-length, and multiple newline-conversion helpers.
• Some intercepted modes have extra runtime dependencies: for example -x2p needs xmllint, -j2p needs python3, and several helpers require perl.
• In local testing, printf '{"a":1}\n' | transmute -j2x -set Set -rec Rec produced a wrapped XML document with <Set><Rec><a>1</a></Rec></Set>.
• If the compiled backend is missing, the wrapper prints explicit download instructions for transmute.<platform>.gz rather than failing silently.