fast and robust BED to GTF/GFF conversion in rust

docs . usage . install . conda

• Converts BED to GTF or GFF/GFF3
• Supports .bed and .bed.gz inputs
• Supports .gtf, .gtf.gz, .gff, .gff3, .gff.gz, and .gff3.gz outputs
• Uses memory-mapped I/O for uncompressed file inputs
• Uses rayon for parallel chunked conversion
• Reads from stdin when --input is omitted
• Writes to stdout when --output is omitted
• Accepts an optional transcript-to-gene mapping file through --isoforms

bed2gtf [OPTIONS]

Options:
  -i, --input <BED>         Input BED path; reads stdin when omitted
  -o, --output <OUTPUT>     Output path; writes stdout when omitted
      --to <gtf|gff>        Output format for stdout; required when --output is absent
  -I, --isoforms <TSV>      Optional transcript-to-gene map
  -t, --type <BED_TYPE>     BED layout: 3, 4, 5, 6, 8, 9, 12 [default: 12]
  -T, --threads <N>         Worker threads [default: logical CPU count]
  -c, --chunks <N>          Parallel chunk size [default: 15000]
  -g, --gz                  Gzip stdout or require a .gz output path
  -L, --level <LEVEL>       Log level: error, warn, info, debug, trace [default: info]
  -h, --help                Print help
  -V, --version             Print version

cargo install bed2gtf

1. get rust
2. run git clone https://github.com/alejandrogzi/bed2gtf.git && cd bed2gtf
3. run cargo run --release -- -i <BED> -o <OUTPUT>

to build the development container image:

1. run git clone https://github.com/alejandrogzi/bed2gtf.git && cd bed2gtf
2. initialize docker with start docker or systemctl start docker
3. build the image docker image build --tag bed2gtf .
4. run docker run --rm -v "[dir_where_your_files_are]:/dir" bed2gtf -i /dir/<BED> -o /dir/<OUTPUT>

to use bed2gtf through Conda just:

1. conda install bed2gtf -c bioconda or conda create -n bed2gtf -c bioconda bed2gtf

to use bed2gtf through Nextflow as a module just:

1. borrow main.nf from here

• If --output is present, the output format is derived from its extension.
• If --output is absent, --to gtf or --to gff is required.
• If the input path is .bed.gz, the output must also be gzip-compressed.
• When writing to stdout, gzip output is enabled automatically for gzip input.
• --gz is mainly useful for stdout. For file output, the path must end in .gz when gzip is requested.

--isoforms is optional.

When provided, it must point to a two-column tab-separated file:

ENST00000335137	ENSG00000186092
ENST00000423372	ENSG00000237613

• Column 1: transcript ID
• Column 2: gene ID

Blank lines and # comments are ignored.

Convert an uncompressed BED12 file to GTF:

bed2gtf --input transcripts.bed --output transcripts.gtf

Convert a gzip-compressed BED file to gzip-compressed GFF3:

bed2gtf --input transcripts.bed.gz --output transcripts.gff3.gz

Write GTF to stdout:

bed2gtf --input transcripts.bed --to gtf

Read from stdin and write GFF to stdout:

cat transcripts.bed | bed2gtf --to gff

Use a transcript-to-gene mapping file:

bed2gtf \
  --input transcripts.bed \
  --output transcripts.gtf \
  --isoforms isoforms.tsv

Enable debug logging:

bed2gtf --input transcripts.bed --output transcripts.gtf --level debug