genome-format-converters 0.1.0

A collection of Python scripts for converting common bioinformatics file formats

Author: Benjamin Narh-Madey

Affiliation: Hittinger Lab, Laboratory of Geenetics University of Wisconsin-Madison

Genome Format Converters

A collection of Python scripts for converting common bioinformatics file formats. Each script follows a simple, uniform interface: you point it to an input directory, and it writes converted files to an output directory.

Table of Contents

• Features
• Installation
• Usage
• Command Reference
  • Annotation Format Conversions
  • Sequence Format Conversions
  • Alignment / Mapping Results
  • Variant Formats (VCF)
  • Phylogenetic Tree Formats
• Scripts Overview
• License
• Contributing

Features

• Uniform interface: all scripts accept --input-dir and --output-dir arguments.
• Batch processing: convert all files of a given type in a directory at once.
• Lightweight: only requires a few well‑maintained Python libraries.
• Well tested: each script has been tested on small example datasets.

Installation

Clone the repository:

bash git clone https://github.com/K-nie/genome-format-converters.git cd genome-format-converters Install the required dependencies:

##bash pip install -r requirements.txt

Note: For scripts that work with BAM or VCF files, you also need pysam (included in requirements.txt).

For BLAST tabular conversion, you need BLAST+ installed separately (optional – only if you generate the input files).

Usage All scripts are used in the same way:

##bash gfc --input-dir INPUT_DIR --output-dir OUTPUT_DIR [options]

The input directory should contain the files you want to convert. The output directory will be created if it doesn’t exist.

Each subcommand processes all files with recognised extensions in the input directory.

Run gfc --help to see all available subcommands, or gfc --help for detailed options.

Command Reference

Annotation Format Conversions

Subcommand Description Example

gff3-to-gtf Convert GFF3 to GTF gfc gff3-to-gtf --input-dir ./gff_files --output-dir ./gtf_output gff3-to-bed Convert GFF3 to 6‑column BED gfc gff3-to-bed --input-dir ./gff_files --output-dir ./bed_output genbank-to-gff3 Convert GenBank to GFF3 gfc genbank-to-gff3 --input-dir ./gbk_files --output-dir ./gff3_output gff3-to-table Convert GFF3 to tab‑separated feature table gfc gff3-to-table --input-dir ./gff_files --output-dir ./table_output gff3-to-protein Extract protein sequences from GFF3 + FASTA gfc gff3-to-protein --input-dir ./data --output-dir ./proteins fasta-gff-to-gbk Convert paired FASTA and GFF3 files to GenBank gfc fasta-gff-to-gbk --input-dir ./data --output-dir ./gbk_output

Sequence Format Conversions

Subcommand Description Example

fasta-to-fastq FASTA → FASTQ with default quality (I) gfc fasta-to-fastq --input-dir ./fasta --output-dir ./fastq fastq-to-fasta FASTQ → FASTA (drop qualities) gfc fastq-to-fasta --input-dir ./fastq --output-dir ./fasta fasta-qual-to-fastq Combine FASTA + QUAL into FASTQ gfc fasta-qual-to-fastq --input-dir ./data --output-dir ./fastq fastq-to-fasta-qual Split FASTQ into FASTA and QUAL gfc fastq-to-fasta-qual --input-dir ./fastq --output-dir ./split fasta-to-table FASTA → two‑column TSV (id, sequence) gfc fasta-to-table --input-dir ./fasta --output-dir ./tables convert-alignment Convert alignment formats (fasta, phylip, nexus, clustal) gfc convert-alignment --input-dir ./aln --output-dir ./phylip --in-format fasta --out-format phylip

Alignment / Mapping Results

Subcommand Description Example

bam-to-bed Convert BAM/SAM to BED6 gfc bam-to-bed --input-dir ./bam_files --output-dir ./bed blast-to-links Convert BLAST tabular (outfmt 6) to link TSV gfc blast-to-links --input-dir ./blast_results --output-dir ./links --min-length 100 --min-identity 30 delta-to-tab Convert MUMmer .delta to tabular coordinates gfc delta-to-tab --input-dir ./delta_files --output-dir ./tables maf-to-xmfa Convert MAF to XMFA (progressiveMauve format) gfc maf-to-xmfa --input-dir ./maf_files --output-dir ./xmfa

Variant Formats (VCF)

Subcommand Description Example

vcf-to-bed Convert VCF to BED intervals gfc vcf-to-bed --input-dir ./vcf_files --output-dir ./bed vcf-to-table Convert VCF to tab‑separated table gfc vcf-to-table --input-dir ./vcf_files --output-dir ./tables vcf-to-consensus Create consensus FASTA from VCF + reference gfc vcf-to-consensus --input-dir ./data --output-dir ./consensus

Phylogenetic Tree Formats

Subcommand Description Example

tree-convert Convert tree formats (newick, nexus, phyloxml) gfc tree-convert --input-dir ./trees --output-dir ./converted --in-format newick --out-format nexus annotate-tree Add alignment sequences to tree (output NEXUS) gfc annotate-tree --tree tree.nwk --aln alignment.fasta --output annotated.nex

Scripts Overview

The underlying Python scripts are located in src/genome_format_converters/converters/. Each script can also be run independently (though the gfc interface is recommended). Below is a quick reference of the scripts and their input/output formats.

Script Description Input extensions Output extension

gff3_to_gtf.py GFF3 → GTF .gff3, .gff .gtf gff3_to_bed.py GFF3 → 6‑column BED .gff3, .gff .bed genbank_to_gff3.py GenBank → GFF3 .gbk, .gb .gff3 gff3_to_table.py GFF3 → tab‑separated feature table .gff3, .gff .tsv gff3_to_protein.py GFF3 + FASTA → protein FASTA .gff3/.gff + .fasta/.fa .faa fasta_to_fastq.py FASTA → FASTQ (with default quality) .fasta, .fa, .fna, .fas .fastq fastq_to_fasta.py FASTQ → FASTA .fastq, .fq .fasta fasta_qual_to_fastq.py Combine FASTA + QUAL → FASTQ .fasta/.fa + .qual .fastq fastq_to_fasta_qual.py Split FASTQ → FASTA + QUAL .fastq, .fq .fasta, .qual convert_alignment.py Alignment format converter (FASTA, PHYLIP, NEXUS, CLUSTAL) any alignment file user‑specified fasta_to_table.py FASTA → two‑column TSV (ID, sequence) .fasta, .fa, .fna, .fas .tsv bam_to_bed.py BAM/SAM → BED6 .bam, .sam .bed blast_tab_to_links.py BLAST tabular (outfmt 6) → simplified link TSV .tab .links.tsv delta_to_tab.py MUMmer .delta → tabular alignment coordinates .delta .tsv maf_to_xmfa.py MAF → XMFA (progressiveMauve format) .maf .xmfa vcf_to_bed.py VCF/BCF → 1‑bp BED intervals .vcf, .vcf.gz, .bcf .bed vcf_to_table.py VCF/BCF → tab‑separated table (TSV) .vcf, .vcf.gz, .bcf .tsv vcf_to_consensus.py VCF + reference FASTA → consensus FASTA per sample .vcf/.vcf.gz + .fasta .fa tree_convert.py Newick ↔ NEXUS ↔ PhyloXML .nwk, .nex, .xml user‑specified annotate_tree.py Add alignment sequences to tree (NEXUS output) .nwk + .fasta (aligned) .nex convert_all_gff_fasta_to_gbk.py FASTA+GFF → GenBank .fasta/.fa + .gff3/.gff .gbk

Testing

All scripts have been tested on small example datasets located in the tests/test_data/ directory. These test files cover the basic functionality of each converter. To run the tests yourself, install the package in development mode (pip install -e .) and execute the example commands from the Command Reference using the provided test data. For instance:

##bash gfc gff3-to-gtf --input-dir tests/test_data --output-dir test_output gfc fasta-to-fastq --input-dir tests/test_data --output-dir test_output

... etc.

License

This project is licensed under the MIT License – see the LICENSE file for details.

Contributing

Contributions are welcome! If you have a new converter or an improvement, please open an issue or submit a pull request.