gff2xml

name	gff2xml
description	Use when converting GFF or GFF3 feature annotations into structured XML for downstream EDirect-style processing.
disable-model-invocation	true
user-invocable	true

gff2xml

Quick Start

• Command: gff2xml [options] < input.gff > output.xml
• Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gff2xml
• Full reference: See references/help.md for detailed usage and options

When To Use This Tool

• Turn GFF/GFF3 feature lines into structured XML with explicit fields and parsed attributes.
• Preserve the common columns (SeqID, Source, Type, Start, End, Score, Strand, Phase) in a machine-friendly XML layout.
• Split semicolon-delimited Attributes into nested XML tags for downstream extraction.

Common Patterns

# 1) Convert a GFF3 file into structured XML
gff2xml < annotations.gff3 > annotations.xml

# 2) Convert and inspect parsed attributes immediately
gff2xml < annotations.gff3 | xtract -pattern GFF -element SeqID Type Start End ID Name

Recommended Workflow

1. Confirm the input really is 9-column GFF/GFF3 with semicolon-delimited attributes.
2. Run gff2xml via stdin redirection so the wrapper can process the stream.
3. Inspect a few output records to confirm the expected XML tags and attribute splitting.
4. Use the XML with xtract or downstream reporting steps once the structure looks right.

Guardrails

• This is not a single binary conversion primitive; it chains tbl2xml, xtract, and transmute, and all of those helpers must be on PATH.
• The wrapper has no real --help / --version path; probing it outside a working EDirect environment mostly yields missing-command noise.
• Attributes are split on semicolons into nested XML tags, so unusual attribute encodings may need spot-checking.
• Because the wrapper does not pass through positional filenames, stdin redirection is the safest invocation pattern.