convert2blastmask

name	convert2blastmask
description	Use when converting lower-case masked FASTA files to masking formats compatible with makeblastdb for BLAST database preparation.
disable-model-invocation	true
user-invocable	true

convert2blastmask

Quick Start

• Command: convert2blastmask -in masked.fa -out mask.asn1 -masking_algorithm <name> -masking_options <text> [options]
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/convert2blastmask
• Full reference: See references/help.md

When To Use This Tool

• Convert lower-case soft-masked FASTA into mask files that makeblastdb can consume.
• Preserve masking provenance by recording the masking program name and options used upstream.
• Emit interval or ASN.1/XML mask representations for BLAST database preparation.
• Carry sequence IDs through with -parse_seqids when the masking data must stay aligned to parsed FASTA identifiers.

Common Patterns

# 1) Convert soft-masked FASTA to the default ASN.1 text format
convert2blastmask \
  -in masked.fa \
  -out masked.asn1.txt \
  -masking_algorithm windowmasker \
  -masking_options "-mk_counts true -ustat counts.obinary"

# 2) Emit interval output for inspection
convert2blastmask \
  -in masked.fa \
  -out masked.interval \
  -outfmt interval \
  -masking_algorithm dust \
  -masking_options "20 64 1"

# 3) Keep parsed FASTA identifiers aligned with downstream BLAST DB creation
convert2blastmask \
  -in masked.fa \
  -out masked.xml \
  -outfmt maskinfo_xml \
  -parse_seqids \
  -masking_algorithm other \
  -masking_options "custom repeat masking"

Recommended Workflow

1. Start from a FASTA whose masked regions are represented in lower case.
2. Record the masking method faithfully with -masking_algorithm and -masking_options; treat those fields as provenance, not decoration.
3. Choose the output format that matches how makeblastdb or your downstream tooling expects mask data.
4. Build the BLAST database immediately afterward so the mask file and FASTA stay synchronized.

Guardrails

• -masking_algorithm and -masking_options are required.
• The input is lower-case masked FASTA, not BED, GFF, or interval text.
• Use BLAST+ style flags such as -help and -version; the common --help pattern is wrong here.
• -parse_seqids only helps if the FASTA deflines are parseable and you will preserve those IDs consistently into makeblastdb.
• The default input and output are stdin and stdout, so explicit -in and -out are safer in batch workflows.