blast-formatter

name	blast-formatter
description	Use when you need to reformat BLAST archive files into different output formats (tabular, HTML, custom) without re-running the BLAST search.
disable-model-invocation	true
user-invocable	true

blast-formatter

Quick Start

• Command: blast_formatter -archive <archive.asn> -outfmt <format> -out <output>
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/blast_formatter
• Version: 2.17.0+
• Full reference: See references/help.md

When To Use This Tool

• Reformat a saved BLAST archive (outfmt 11) into tabular, XML, JSON, SAM, pairwise text, or HTML output.
• Render the same search result in multiple formats without recomputing the alignment search.
• Pull results by RID after a remote BLAST job finishes.
• Define custom tabular field lists once the archive already exists.

Common Patterns

# 1) Reformat a saved archive as tabular output
blast_formatter \
  -archive search.asn \
  -outfmt "6 qaccver saccver pident length evalue bitscore" \
  -out hits.tsv

# 2) Generate an HTML report from the same archive
blast_formatter \
  -archive search.asn \
  -html \
  -outfmt 0 \
  -out report.html

# 3) Retrieve and format a completed remote search by RID
blast_formatter \
  -rid RID_VALUE \
  -outfmt 5 \
  -out result.xml

Recommended Workflow

1. Save BLAST searches as archive format (-outfmt 11) whenever you may want multiple downstream renderings.
2. Reformat the archive into the specific machine-readable or human-readable representation you need.
3. Use custom field lists with -outfmt 6, 7, 10, 17, or 20 instead of accepting defaults blindly.
4. Keep the original archive so you can regenerate other views later.

Guardrails

• -archive and -rid are mutually exclusive inputs.
• This tool does not rerun BLAST; it only formats an archive or completed remote request.
• -max_target_seqs cannot be combined with -num_descriptions or -num_alignments.
• The command name on disk is blast_formatter even though this skill is named blast-formatter.