blst2gm

name	blst2gm
description	Use when converting compatible BLAST annotation XML/ASN streams into a compact gene-markup-style table for downstream EDirect interval helpers.
disable-model-invocation	true
user-invocable	true

blst2gm

Quick Start

• Command: cat blast_input.asn | blst2gm
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blst2gm
• I/O shape: reads BLAST annotation data on stdin and writes a compact tab-delimited summary

When To Use This Tool

• Collapse compatible BLAST annotation records into a small tabular representation.
• Prepare BLAST-derived intervals for downstream helpers such as gm2ranges or gm2segs.
• Stay inside an EDirect / xtract pipeline instead of manually traversing annot_E structures.
• Filter specifically for the BLASTN - mrna annotation class used by this wrapper.

Common Patterns

# 1) Convert a compatible BLAST annotation stream
cat smear.asn | blst2gm > smear.tsv

# 2) Feed the result into range-oriented downstream helpers
cat smear.asn | blst2gm | gm2ranges

# 3) Inspect the compact columns directly
cat smear.asn | blst2gm | column -ts $'\t'

Recommended Workflow

1. Start from BLAST annotation data in the structure expected by the wrapper's xtract recipe.
2. Pipe that stream into blst2gm and inspect the emitted accession, score, starts, lengths, and strand fields.
3. Continue into gm2ranges or gm2segs if you need interval normalization or segment reporting.
4. Keep the original BLAST annotation source around if you may need richer metadata later.

Guardrails

• The wrapper has no option parsing or built-in help path.
• Empty stdin fails with the underlying xtract error No data supplied to xtract from stdin or file.
• The source recipe explicitly filters for annotations labeled BLASTN - mrna; other BLAST types are ignored.
• Output fields are condensed with pipe-separated multi-value columns rather than expanded row-per-segment tables.
• The wrapper depends on xtract being on PATH.