gffx 0.1.0

An ultra-fast and memory-efficient toolkit for querying GFF files, written with Rust
Documentation
gffx-0.1.0 has been yanked.

GFFx Command Line Manual

GFFx is a high-performance, Rust-based toolkit for extracting and querying annotations from GFF3 files. It supports fast indexing and feature retrieval with several subcommands.

Basic Usage

gffx <SUBCOMMAND> [OPTIONS]

Available subcommands:

  • [index] Build index files
  • [intersect] Extract features by region
  • [extract] Extract features by ID
  • [search] Search features by attribute

index: Build Index for GFF

Builds index files from a GFF file to accelerate downstream operations.

gffx index [OPTIONS] --input <INPUT>

Options:

Option Description
-i, --input Input GFF file
-a, --attribute Attribute key to extract (default: gene_name)
-v, --verbose Enable verbose output
-h, --help Print help

intersect: Extract Features by Region

Extracts models intersecting with regions from a GFF file, either from a single region or a BED file.

gffx intersect [OPTIONS] --input <INPUT> <--region <REGION>|--bed <BED>>

Options: Required

Option Description
-i, --input <INPUT> Input GFF file path
(one of)
-r, --region <REGION> Single region in chr:start-end format
-b, --bed <BED> BED file containing multiple regions

Optional

Option Description
-o, --output <OUT> Output file path (default: stdout)
-v, --invert Invert selection (exclude matched features)
-T, --types <TYPES> Filter output to include only features of specified types (e.g., gene,exon)
-t, --threads <N> Number of threads to use (default: 4)
-V, --verbose Enable verbose output
-h, --help Show help message
(one of)
-c, --contained Only keep features fully contained within the region
-C, --contains-region Only keep features that fully contain the region
-O, --overlap Keep features that partially or fully overlap (default mode)

extract: Extract Features by ID

Extracts annotation models by feature ID(s), including their parent models.

gffx extract [OPTIONS] --input <INPUT> <--feature-file <FEATURE_FILE>|--feature-id <FEATURE_ID>>```

Options:

Required

Option Description
-i, --input <INPUT> Input GFF file path
(one of)
-f, --feature-id <FEATURE_ID> Extrach by a single feature id
-F, --feature-file <FEATURE_FILE> Extrach by a BED file containing multiple regions

Optional

Option Description
-o, --output <OUT> Output file path (default: stdout)
-T, --types <TYPES> Filter output to include only features of specified types (e.g., gene,exon)
-d, --descendants-only Only extract feature(s) and their/its descendants
-t, --threads <N> Number of threads to use (default: 4)
-V, --verbose Enable verbose output
-h, --help Show help message

search: Search Features by Attribute

Searches for features using a specified attribute value and retrieves the full annotation models.

gffx search -a geneX -i input.gff

Options:

Required

Option Description
-i, --input <INPUT> Input GFF file path
(one of)
-a, --attr ATTRIBUTE_VALUE> Search a single attribute value/pattern
-A, --attr-list <ATTRIBUTE_LIST> Search attribute values/patterns defined in a text file

Optional

Option Description
-o, --output <OUT> Output file path (default: stdout)
-r, --regex <REGEX> Enable regex matching for attribute values
-T, --types <TYPES> Filter output to include only features of specified types (e.g., gene,exon)
-t, --threads <N> Number of threads to use (default: 4)
-V, --verbose Enable verbose output
-h, --help Show help message

💡 Example Use Cases

# Build index
gffx index -i genes.gff -a gene_name

# Extract all features overlapping with a region
gffx intersect --region chr1:10000-20000 -i genes.gff -o out.gff

# Extract models from a list of gene IDs
gffx extract --feature-file genes.txt -i genes.gff -o subset.gff

# Search by gene name and extract the full model
gffx search -a TP53 -i genes.gff -o tp53_model.gff

🛠️ Notes

  • Make sure you run gffx index before using intersect, extract, or search.
  • All subcommands are optimized for multi-threaded execution where applicable.