bioconvert 0.5.1

convert between bioinformatics formats

Bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

contributions:

Want to add a convertor ? Please join https://github.com/bioconvert/bioconvert/issues/1

issues:

Please use https://github.com/bioconvert/bioconvert/issues

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 March 2022, we had 48 formats, 98 direct conversions (125 different methods).

Installation

In order to install bioconvert, you can use pip:

pip install bioconvert

We also provide releases on bioconda (http://bioconda.github.io/):

conda install bioconvert

and Singularity container are available. See http://bioconvert.readthedocs.io/en/master/user_guide.html#installation for details.

Usage

From the command line, you can convert a FastQ file into a FastA file as follows (compressed or not):

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

For help, just type:

bioconvert --help
bioconvert fastq2fasta --help

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

Conversion table

Converters	CI testing	Benchmarking
abi2fasta
abi2fastq
abi2qual
bam2bedgraph
bam2bigwig
bam2cov
bam2cram
bam2fasta
bam2fastq
bam2json
bam2sam
bam2tsv
bam2wiggle
bcf2vcf
bcf2wiggle
bed2wiggle
bedgraph2bigwig
bedgraph2cov
bedgraph2wiggle
bigbed2bed
bigbed2wiggle
bigwig2bedgraph
bigwig2wiggle
bplink2plink
bplink2vcf
bz22gz
clustal2fasta
clustal2nexus
clustal2phylip
clustal2stockholm
cram2bam
cram2fasta
cram2fastq
cram2sam
csv2tsv
csv2xls
dsrc2gz
embl2fasta
embl2genbank
fasta2clustal
fasta2faa
fasta2fasta_agp
fasta2fastq
fasta2genbank
fasta2nexus
fasta2phylip
fasta2twobit
fasta_qual2fastq
fastq2fasta		available
fastq2fasta_qual
fastq2qual
genbank2embl
genbank2fasta
genbank2gff3
gfa2fasta
gff22gff3
gff32gff2
gz2bz2
gz2dsrc
json2yaml
maf2sam
newick2nexus
newick2phyloxml
nexus2clustal
nexus2fasta
nexus2newick
nexus2phylip
nexus2phyloxml
ods2csv
phylip2clustal
phylip2fasta
phylip2nexus
phylip2stockholm
phylip2xmfa
phyloxml2newick
phyloxml2nexus
plink2bplink
plink2vcf
sam2bam
sam2cram
sam2paf
scf2fasta
scf2fastq
sra2fastq
stockholm2clustal
stockholm2phylip
tsv2csv
twobit2fasta
vcf2bcf
vcf2bed
vcf2bplink
vcf2plink
vcf2wiggle
wig2bed
xls2csv
xlsx2csv
xmfa2phylip
yaml2json

Contributors

Setting up and maintaining Bioconvert has been possible thanks to users and contributors. Thanks to all:

Changes

Version	Description
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)