bioconvert 0.6.0

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

bioconvert is a Python library but depends on many third-party software (e.g., samtools). Therefore, the bioconda method is the recommended one for end-users because it installs bioconvert and all its dependencies. If you choose the pip method, only the bioconvert Python package will be installed.

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	Default method
abi2fasta		BIOPYTHON
abi2fastq		BIOPYTHON
abi2qual		BIOPYTHON
bam2bedgraph		BEDTOOLS
bam2bigwig
bam2cov		BEDTOOLS
bam2cram		SAMTOOLS
bam2fasta		SAMTOOLS
bam2fastq		SAMTOOLS
bam2json		BAMTOOLS
bam2sam		SAMBAMBA
bam2tsv		SAMTOOLS
bam2wiggle		WIGGLETOOLS
bcf2vcf		BCFTOOLS
bcf2wiggle		WIGGLETOOLS
bed2wiggle		WIGGLETOOLS
bedgraph2bigwig		UCSC
bedgraph2cov		BIOCONVERT
bedgraph2wiggle		WIGGLETOOLS
bigbed2bed		DEEPTOOLS
bigbed2wiggle		WIGGLETOOLS
bigwig2bedgraph		DEEPTOOLS
bigwig2wiggle		WIGGLETOOLS
bplink2plink		PLINK
bplink2vcf		PLINK
bz22gz		Unix commands
clustal2fasta		BIOPYTHON
clustal2nexus		GOALIGN
clustal2phylip		BIOPYTHON
clustal2stockholm		BIOPYTHON
cram2bam		SAMTOOLS
cram2fasta		SAMTOOLS
cram2fastq		SAMTOOLS
cram2sam		SAMTOOLS
csv2tsv
csv2xls
dsrc2gz
embl2fasta		BIOPYTHON
embl2genbank		BIOPYTHON
fasta2clustal		BIOPYTHON
fasta2faa		BIOCONVERT
fasta2fasta_agp		BIOCONVERT
fasta2fastq		PYSAM
fasta2genbank		BIOCONVERT
fasta2nexus		GOALIGN
fasta2phylip		BIOPYTHON
fasta2twobit		UCSC
fasta_qual2fastq		PYSAM
fastq2fasta		BIOCONVERT available
fastq2fasta_qual		BIOCONVERT
fastq2qual		READFQ
genbank2embl		BIOPYTHON
genbank2fasta		BIOPYTHON
genbank2gff3		BIOCODE
gfa2fasta		BIOCONVERT
gff22gff3		BIOCONVERT
gff32gff2		BIOCONVERT
gz2bz2
gz2dsrc
json2yaml
maf2sam		?
newick2nexus		GOTREE
newick2phyloxml		GOTREE
nexus2clustal		GOALIGN
nexus2fasta		BIOPYTHON
nexus2newick		GOTREE
nexus2phylip		GOALIGN
nexus2phyloxml		GOTREE
ods2csv
phylip2clustal		BIOPYTHON
phylip2fasta		BIOPYTHON
phylip2nexus		GOALIGN
phylip2stockholm		BIOPYTHON
phylip2xmfa		BIOPYTHON
phyloxml2newick		GOTREE
phyloxml2nexus		GOTREE
plink2bplink		PLINK
plink2vcf		PLINK
sam2bam		SAMTOOLS
sam2cram		SAMTOOLS
sam2paf		BIOCONVERT
scf2fasta		BIOCONVERT
scf2fastq		BIOCONVERT
sra2fastq		FASTQDUMP
stockholm2clustal		BIOPYTHON
stockholm2phylip		BIOPYTHON
tsv2csv
twobit2fasta		DEEPTOOLS
vcf2bcf		BCFTOOLS
vcf2bed		BIOCONVERT
vcf2bplink		PLINK
vcf2plink		PLINK
vcf2wiggle		WIGGLETOOLS
wig2bed		BEDOPS
xls2csv
xlsx2csv
xmfa2phylip		BIOPYTHON
yaml2json

Contributors

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

Changes

Version	Description
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)