Bioconvert ##########
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
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:contributions: Want to add a convertor ? Please join https://github.com/bioconvert/bioconvert/issues/1
Overview ########
Life science uses many different formats. They may be old, or with complex syntax and converting those formats may be a challenge. Bioconvert aims at providing a common tool / interface to convert life science data formats from one to another.
Many conversion tools already exist but they may be dispersed, focused on few specific formats, difficult to install, or not optimised. With Bioconvert, we plan to cover a wide spectrum of format conversions; we will re-use existing tools when possible and provide facilities to compare different conversion tools or methods via benchmarking. New implementations are provided when considered better than existing ones.
In Jan 2023, we had 50 formats, 100 direct conversions available.
.. image:: https://raw.githubusercontent.com/bioconvert/bioconvert/main/doc/conversion.png :width: 80%
Installation ###############
BioConvert is developped in Python. Please use conda or any Python environment manager to install BioConvert using the pip command::
pip install bioconvert
50% of the conversions should work out of the box. However, many conversions require external tools. This is why we recommend to use a conda environment. In particular, most external tools are available on the bioconda channel. For instance if you want to convert a SAM file to a BAM file you would need to install samtools as follow::
conda install -c bioconda samtools
Since bioconvert is available on bioconda <https://bioconda.github.io>_ on solution that installs BioConvert and all its dependencies is to use conda/mamba::
conda env create --name bioconvert mamba
conda activate bioconvert
mamba install bioconvert
bioconvert --help
See the Installation section for more details and alternative solutions (docker, singularity).
Quick Start ############## There are many conversions available. Type::
bioconvert --help
to get a list of valid method of conversions. Taking the example of a conversion from a FastQ file into
a FastA file, you could do the conversion as follows::
bioconvert fastq2fasta input.fastq output.fasta
bioconvert fastq2fasta input.fq output.fasta
bioconvert fastq2fasta input.fq.gz output.fasta.gz
bioconvert fastq2fasta input.fq.gz output.fasta.bz2
When there is no ambiguity, you can be implicit::
bioconvert input.fastq output.fasta
The default method of conversion is used but you may use another one. Checkout the available methods with::
bioconvert fastq2fasta --show-methods
For more help about a conversion, just type::
bioconvert fastq2fasta --help
and more generally::
bioconvert --help
You may also call BioConvert from a Python shell::
# import a converter
from bioconvert.fastq2fasta import FASTQ2FASTA
# Instanciate with infile/outfile names
convert = FASTQ2FASTA(infile, outfile)
# the conversion itself:
convert()
Available Converters #######################
.. list-table:: Conversion table :widths: 20 40 40 :header-rows: 1
* - Converters
- CI testing
- Default method
* - `abi2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `abi2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2fastq.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `abi2qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.abi2qual>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/abi2qual.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/abi2qual.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2bedgraph <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2bedgraph>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bedgraph.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bedgraph.yml
- `BEDTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2bigwig <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2bigwig>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bigwig.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2bigwig.yml
- `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2cov <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2cov>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cov.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cov.yml
- `BEDTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2cram <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2cram>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cram.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2cram.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fasta.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2fastq.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2json <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2json>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2json.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2json.yml
- `BAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2sam>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2sam.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2sam.yml
- `SAMBAMBA <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2tsv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2tsv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2tsv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2tsv.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bam2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bam2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bam2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bam2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bcf2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bcf2vcf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2vcf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2vcf.yml
- `BCFTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bcf2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bcf2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bcf2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bed2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bed2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bed2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bed2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2bigwig <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2bigwig>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2bigwig.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2bigwig.yml
- `UCSC <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2cov <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2cov>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2cov.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2cov.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bedgraph2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bedgraph2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bedgraph2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigbed2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigbed2bed>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2bed.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2bed.yml
- `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigbed2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigbed2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bigbed2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigwig2bedgraph <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigwig2bedgraph>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2bedgraph.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2bedgraph.yml
- `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bigwig2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bigwig2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bigwig2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bplink2plink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bplink2plink>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2plink.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2plink.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bplink2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bplink2vcf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2vcf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bplink2vcf.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `bz22gz <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.bz22gz>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/bz22gz.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/bz22gz.yml
- Unix commands
* - `clustal2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2nexus>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2nexus.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2nexus.yml
- `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2phylip>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2phylip.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2phylip.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `clustal2stockholm <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.clustal2stockholm>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2stockholm.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/clustal2stockholm.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2bam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2bam>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2bam.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2bam.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fasta.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2fastq.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `cram2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.cram2sam>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/cram2sam.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/cram2sam.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `csv2tsv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.csv2tsv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/csv2tsv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/csv2tsv.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `csv2xls <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.csv2xls>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/csv2xls.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/csv2xls.yml
- Pandas
* - `dsrc2gz <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.dsrc2gz>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/dsrc2gz.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/dsrc2gz.yml
- DSRC software
* - `embl2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.embl2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/embl2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/embl2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `embl2genbank <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.embl2genbank>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/embl2genbank.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/embl2genbank.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2clustal>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2clustal.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2clustal.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2faa <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2faa>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2faa.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2faa.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2fasta_agp <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2fasta_agp>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fasta_agp.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fasta_agp.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2fastq.yml
- `PYSAM <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2genbank <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2genbank>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2genbank.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2genbank.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2nexus>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2nexus.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2nexus.yml
- `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2phylip>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2phylip.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2phylip.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta2twobit <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta2twobit>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2twobit.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta2twobit.yml
- `UCSC <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fasta_qual2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fasta_qual2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fasta_qual2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fasta_qual2fastq.yml
- `PYSAM <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fastq2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_ `available <_static/benchmark_fastq2fasta.png>`_
* - `fastq2fasta_qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2fasta_qual>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta_qual.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2fasta_qual.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `fastq2qual <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.fastq2qual>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2qual.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/fastq2qual.yml
- `READFQ <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2embl <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2embl>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2embl.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2embl.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `genbank2gff3 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.genbank2gff3>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2gff3.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/genbank2gff3.yml
- `BIOCODE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gfa2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gfa2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gfa2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gfa2fasta.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff22gff3 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff22gff3>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff22gff3.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gff22gff3.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff32gff2 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff32gff2>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gff2.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gff2.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gff32gtf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gff32gtf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gtf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gff32gtf.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `gz2bz2 <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gz2bz2>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gz2bz2.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gz2bz2.yml
- pigz/pbzip2 software
* - `gz2dsrc <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.gz2dsrc>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/gz2dsrc.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/gz2dsrc.yml
- DSRC software
* - `json2yaml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.json2yaml>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/json2yaml.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/json2yaml.yml
- Python
* - `maf2sam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.maf2sam>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/maf2sam.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/maf2sam.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `newick2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.newick2nexus>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/newick2nexus.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/newick2nexus.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `newick2phyloxml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.newick2phyloxml>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/newick2phyloxml.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/newick2phyloxml.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2clustal>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2clustal.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2clustal.yml
- `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2newick <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2newick>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2newick.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2newick.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2phylip>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phylip.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phylip.yml
- `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `nexus2phyloxml <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.nexus2phyloxml>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phyloxml.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/nexus2phyloxml.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `ods2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.ods2csv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/ods2csv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/ods2csv.yml
- pyexcel library
* - `pdb2faa <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.pdb2faa>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/pdb2faa.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/pdb2faa.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2clustal>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2clustal.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2clustal.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2fasta.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2nexus>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2nexus.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2nexus.yml
- `GOALIGN <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2stockholm <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2stockholm>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2stockholm.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2stockholm.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phylip2xmfa <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phylip2xmfa>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2xmfa.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phylip2xmfa.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phyloxml2newick <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phyloxml2newick>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2newick.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2newick.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `phyloxml2nexus <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.phyloxml2nexus>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2nexus.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/phyloxml2nexus.yml
- `GOTREE <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `plink2bplink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.plink2bplink>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/plink2bplink.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/plink2bplink.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `plink2vcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.plink2vcf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/plink2vcf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/plink2vcf.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2bam <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2bam>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2bam.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2bam.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2cram <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2cram>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2cram.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2cram.yml
- `SAMTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sam2paf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sam2paf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sam2paf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/sam2paf.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `scf2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.scf2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fasta.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `scf2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.scf2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/scf2fastq.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `sra2fastq <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.sra2fastq>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/sra2fastq.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/sra2fastq.yml
- `FASTQDUMP <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `stockholm2clustal <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.stockholm2clustal>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2clustal.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2clustal.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `stockholm2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.stockholm2phylip>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2phylip.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/stockholm2phylip.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `tsv2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.tsv2csv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/tsv2csv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/tsv2csv.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `twobit2fasta <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.twobit2fasta>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/twobit2fasta.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/twobit2fasta.yml
- `DEEPTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bcf <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bcf>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bcf.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bcf.yml
- `BCFTOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bed>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bed.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bed.yml
- `BIOCONVERT <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2bplink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2bplink>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bplink.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2bplink.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2plink <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2plink>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2plink.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2plink.yml
- `PLINK <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `vcf2wiggle <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.vcf2wiggle>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2wiggle.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/vcf2wiggle.yml
- `WIGGLETOOLS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `wig2bed <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.wig2bed>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/wig2bed.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/wig2bed.yml
- `BEDOPS <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `xls2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xls2csv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xls2csv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/xls2csv.yml
-
* - `xlsx2csv <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xlsx2csv>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xlsx2csv.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/xlsx2csv.yml
- Pandas library
* - `xmfa2phylip <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.xmfa2phylip>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/xmfa2phylip.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/xmfa2phylip.yml
- `BIOPYTHON <https://bioconvert.readthedocs.io/en/main/bibliography.html>`_
* - `yaml2json <https://bioconvert.readthedocs.io/en/main/ref_converters.html#module-bioconvert.yaml2json>`_
- .. image:: https://github.com/bioconvert/bioconvert/actions/workflows/yaml2json.yml/badge.svg
:target: https://github.com/bioconvert/bioconvert/actions/workflows/yaml2json.yml
- Pandas library
Contributors ############
Setting up and maintaining Bioconvert has been possible thanks to users and contributors. Thanks to all:
.. image:: https://contrib.rocks/image?repo=bioconvert/bioconvert :target: https://github.com/bioconvert/bioconvert/graphs/contributors
Changes ########
========= ==============================================================================
Version Description
========= ==============================================================================
1.1.1 * Fix benchmark labels.
* NEW: fast52pod5 conversion
* FIX: set goalign and gotree instead of go requirements
1.1.0 * Implement ability to benchmark the CPU and memory usage (not just time)
benchmark incorporates CPU/memory usage
1.0.0 * Fix bam2fastq for paired data that computed useless intermediate file
https://github.com/bioconvert/bioconvert/issues/325
* more realistic fastq simulator
* pin openpyxl to <=3.0.10 to prevent regression error in v3.1.0
0.6.3 * add picard method in bam2sam
* Fixed all CI workflows to use mamba
* drop python3.7 support and add 3.10 support
* update bedops test file to fit the latest bedops 2.4.41 version
* revisit logging system
0.6.2 * added gff3 to gtf conversion.
* Added pdb to faa conversion
* Added missing --reference argument to the cram2sam conversion
0.6.1 * output file can be in sub-directories allowing syntax such as
'bioconvert fastq2fasta test.fastq outputs/test.fasta
* fix all CI actions
* add more examples as notebooks in ./examples
* add a Snakefile for the paper in ./doc/Snakefile_paper
0.6.0 * Fix bug in bam2sam (method sambamba)
* Fix graph layout
* add threading in fastq2fasta (seqkit method)
* multibenchmark feature added
* stable version used for web interface
0.5.2 * Update requirements and environment.yml and add a conda spec-file.txt file
0.5.1 * add genbank2gff3 requirement material in bioconvert.utils.biocode
0.5.0 * Add CI actions for all converters
* remove sniffer (now in biosniff on pypi https://pypi.org/project/biosniff/)
* A complete benchmarking suite (see doc/Snakefile_benchmark file and
benchmarking)
* documentation and tests for all converters
* removed the validators (we assume intputs are correct)
0.4.X * (aug 2019) added nexus2fasta, cram2fasta, fasta2faa ... ; 1-to-many and
many-to-one converters are now part of the API.
0.3.X may 2019. new methods abi2qual, bigbed2bed, etc. added --threads option
0.2.X aug 2018. abi2fastx, bioconvert_stats tool added
0.1.X major refactoring to have subcommands with implicit/explicit mode
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FAQs
convert between bioinformatics formats
We found that bioconvert demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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