blst2tkns

name	blst2tkns
description	Use when turning EDirect-style BLAST XML alignment blocks into a token stream for downstream shell or xtract-based parsing.
disable-model-invocation	true
user-invocable	true

blst2tkns

EDirect shell wrapper over xtract that reads Seq-align-set_E XML and emits a compact label/value token stream for exon-alignment records.

Quick Start

• Command: blst2tkns
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blst2tkns
• Environment prerequisite: add /home/vimalinx/miniforge3/envs/bio/bin to PATH so sibling tools such as xtract are resolvable

When To Use This Tool

• Convert Seq-align-set_E XML into a lighter token stream for shell pipelines.
• Pull out per-alignment values such as running index, score, start, stop, strand, and nested parts/* content.
• Bridge BLAST-derived XML that already lives in an EDirect / xtract workflow into simpler downstream parsing.
• Use this only for the expected XML shape; it is not a generic BLAST tabular, plain-text, or FASTA converter.

Common Patterns

# 1) Tokenize an existing Seq-align-set_E XML file
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

blst2tkns < seq-align-set.xml > align.tokens.txt

# 2) Inspect the first emitted tokens before scaling up
export PATH=/home/vimalinx/miniforge3/envs/bio/bin:$PATH

blst2tkns < seq-align-set.xml | sed -n '1,30p'

Recommended Workflow

1. Confirm the upstream XML actually contains Seq-align-set_E records before blaming the wrapper for empty output.
2. Activate the bio environment or prepend /home/vimalinx/miniforge3/envs/bio/bin to PATH so xtract is available.
3. Run the wrapper on a small sample and inspect the emitted labels before wiring it into a larger pipeline.
4. Feed the token stream to your next shell / EDirect stage once the field order matches what you expect.

Guardrails

• The script is just a one-line xtract recipe. Without the bio bin directory on PATH, it fails immediately with xtract: command not found.
• There is no standalone help path here. With dependencies available, blst2tkns -help still falls through to xtract and errors on missing input.
• With xtract available but no XML input, the live failure is No data supplied to xtract from stdin or file.
• Source inspection shows it hard-codes emission of index, score, start, stop, strand, nested parts/* tokens, and a terminating end 0 marker. If your XML schema differs, output may be partial or empty.