2023-07-04

ライフサイエンスのための包括的なフォーマットコンバーター BioConvert

2023/07/04 追記

　バイオインフォマティクスは、長年にわたって開発されてきた数多くの標準やフォーマットで知られる分野である。このフォーマットの多さは時に補完的であり、しばしば冗長であるため、バイオインフォマティクスのデータ解析者に多くの課題を投げかけている。彼らは常に、データを適切なフォーマットに変換するための最適なツールを見つける必要があり、それはしばしば複雑で技術的、時間のかかる作業となる。さらに、このような小さな、しかし重要な作業は、再現性を持たせることが難しい場合が多い。このような困難を克服するために、本著者らはBioConvertを始めた。これは、生命科学データのあるフォーマットから別のフォーマットへの変換を容易にするための共同プロジェクトである。BioConvertは、既存のソフトウェアを単一のフレームワーク内に集約し、必要に応じてオリジナルのコードで補完する。BioConvertは共通のインターフェースを提供することで、何十ものソフトウェアを学ぶ必要がなく、ユーザーエクスペリエンスをより合理的にしている。現在、BioConvertはアライメント、シーケンス、系統、バリアントコールなどの分野で約50のフォーマットと100の直接変換をサポートしている。エンドユーザーにとって有用であるだけでなく、BioConvertは開発者にとっても、多数の変換ツールを評価・比較するための普遍的なベンチマークフレームワークとして活用することができる。さらに、BioConvertのオンラインユーザーフレンドリーなインターフェースを実装したウェブサーバーを提供し、コミュニティでの直接利用を可能にしている。

Documentation

https://bioconvert.readthedocs.io/en/dev/

Format（バイオインフォマティクスでよく使用されるフォーマットについて解説している）

https://bioconvert.readthedocs.io/en/dev/formats.html

With plenty of colleagues, we are happy to introduce bioconvert, a software to convert bioinformatics files from one format to another. bioconvert currently includes 50 formats and 100 converters. pic.twitter.com/jXI68WyZ6w
— Yoann Dufresne (@yoann_dufresne) March 23, 2023

インストール

ubuntu18にてcondaを使って導入した。

Github

#conda(link) (依存が多いので10分くらいかかる)
mamba create -n bioconvert -y
conda activate bioconvert
mamba install -c bioconda bioconvert -y

#pip(pypi 一部の変換ではsamtoolsも必要)
pip install bioconvert

#Docker(dockerhub)
docker pull bioconvert/bioconvert:0.6.1

 #singularity（Apptainer）のイメージもダウンロードできる

> bioconvert --help

$ bioconvert -h

usage: bioconvert [-h] [-v {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--dependency-report] [-a] [--version] [--conversion-graph [{cytoscape,cytoscape-all}]]

{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,fastq2fasta_qual,fastq2qual,genbank2embl,genbank2fasta,genbank2gff3,gfa2fasta,gff22gff3,gff32gff2,gff32gtf,gz2bz2,gz2dsrc,json2yaml,maf2sam,newick2nexus,newick2phyloxml,nexus2clustal,nexus2fasta,nexus2newick,nexus2phylip,nexus2phyloxml,ods2csv,pdb2faa,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}

...

positional arguments:

sub-command help

abi2fasta abi to-> fasta (1 methods)

abi2fastq abi to-> fastq (1 methods)

abi2qual abi to-> qual (1 methods)

bam2bedgraph bam to-> bedgraph (2 methods)

bam2bigwig bam to-> bigwig (2 methods)

bam2cov bam to-> cov (2 methods)

bam2cram bam to-> cram (1 methods)

bam2fasta bam to-> fasta (1 methods)

bam2fastq bam to-> fastq (2 methods)

bam2json bam to-> json (1 methods)

bam2sam bam to-> sam (4 methods)

bam2tsv bam to-> tsv (2 methods)

bam2wiggle bam to-> wiggle (1 methods)

bcf2vcf bcf to-> vcf (1 methods)

bcf2wiggle bcf to-> wiggle (1 methods)

bed2wiggle bed to-> wiggle (1 methods)

bedgraph2bigwig bedgraph to-> bigwig (1 methods)

bedgraph2cov bedgraph to-> cov (1 methods)

bedgraph2wiggle bedgraph to-> wiggle (1 methods)

bigbed2bed bigbed to-> bed (1 methods)

bigbed2wiggle bigbed to-> wiggle (1 methods)

bigwig2bedgraph bigwig to-> bedgraph (2 methods)

bigwig2wiggle bigwig to-> wiggle (1 methods)

bplink2plink bplink to-> plink (1 methods)

bplink2vcf bplink to-> vcf (1 methods)

bz22gz bz2 to-> gz (2 methods)

clustal2fasta clustal to-> fasta (3 methods)

clustal2nexus clustal to-> nexus (1 methods)

clustal2phylip clustal to-> phylip (2 methods)

clustal2stockholm clustal to-> stockholm (2 methods)

cram2bam cram to-> bam (1 methods)

cram2fasta cram to-> fasta (1 methods)

cram2fastq cram to-> fastq (1 methods)

cram2sam cram to-> sam (1 methods)

csv2tsv csv to-> tsv (3 methods)

csv2xls csv to-> xls (2 methods)

dsrc2gz dsrc to-> gz (1 methods)

embl2fasta embl to-> fasta (2 methods)

embl2genbank embl to-> genbank (2 methods)

fasta2clustal fasta to-> clustal (3 methods)

fasta2faa fasta to-> faa (1 methods)

fasta2fasta_agp fasta to-> fasta_agp (1 methods)

fasta2fastq fasta to-> fastq (1 methods)

fasta2genbank fasta to-> genbank (3 methods)

fasta2nexus fasta to-> nexus (1 methods)

fasta2phylip fasta to-> phylip (3 methods)

fasta2twobit fasta to-> twobit (1 methods)

fasta_qual2fastq fasta_qual to-> fastq (1 methods)

fastq2fasta fastq to-> fasta (9 methods)

fastq2fasta_qual fastq to-> fasta_qual (1 methods)

fastq2qual fastq to-> qual (1 methods)

genbank2embl genbank to-> embl (2 methods)

genbank2fasta genbank to-> fasta (3 methods)

genbank2gff3 genbank to-> gff3 (1 methods)

gfa2fasta gfa to-> fasta (2 methods)

gff22gff3 gff2 to-> gff3 (1 methods)

gff32gff2 gff3 to-> gff2 (1 methods)

gff32gtf gff3 to-> gtf (1 methods)

gz2bz2 gz -to-> bz2 (3 methods)

gz2dsrc gz -to-> dsrc (1 methods)

json2yaml json to-> yaml (1 methods)

maf2sam maf to-> sam (1 methods)

newick2nexus newick to-> nexus (1 methods)

newick2phyloxml newick to-> phyloxml (1 methods)

nexus2clustal nexus to-> clustal (3 methods)

nexus2fasta nexus to-> fasta (3 methods)

nexus2newick nexus to-> newick (2 methods)

nexus2phylip nexus to-> phylip (1 methods)

nexus2phyloxml nexus to-> phyloxml (1 methods)

ods2csv ods to-> csv (1 methods)

pdb2faa pdb to-> faa (1 methods)

phylip2clustal phylip to-> clustal (2 methods)

phylip2fasta phylip to-> fasta (3 methods)

phylip2nexus phylip to-> nexus (1 methods)

phylip2stockholm phylip to-> stockholm (2 methods)

phylip2xmfa phylip to-> xmfa (1 methods)

phyloxml2newick phyloxml to-> newick (1 methods)

phyloxml2nexus phyloxml to-> nexus (1 methods)

plink2bplink plink to-> bplink (1 methods)

plink2vcf plink to-> vcf (1 methods)

sam2bam sam to-> bam (1 methods)

sam2cram sam to-> cram (1 methods)

sam2paf sam to-> paf (1 methods)

scf2fasta scf to-> fasta (1 methods)

scf2fastq scf to-> fastq (1 methods)

sra2fastq sra to-> fastq (1 methods)

stockholm2clustal stockholm to-> clustal (2 methods)

stockholm2phylip stockholm to-> phylip (2 methods)

tsv2csv tsv to-> csv (3 methods)

twobit2fasta twobit to-> fasta (2 methods)

vcf2bcf vcf to-> bcf (1 methods)

vcf2bed vcf to-> bed (1 methods)

vcf2bplink vcf to-> bplink (1 methods)

vcf2plink vcf to-> plink (1 methods)

vcf2wiggle vcf to-> wiggle (1 methods)

wig2bed wig to-> bed (1 methods)

xls2csv xls to-> csv (2 methods)

xlsx2csv xlsx to-> csv (2 methods)

xmfa2phylip xmfa to-> phylip (1 methods)

yaml2json yaml to-> json (1 methods)

options:

-h, --help show this help message and exit

-v {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --verbosity {DEBUG,INFO,WARNING,ERROR,CRITICAL}

Set the outpout verbosity. Same as --level

-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --level {DEBUG,INFO,WARNING,ERROR,CRITICAL}

Set the outpout verbosity. Same as --verbosity

--dependency-report Output all bioconvert dependencies in json and exit

-a, --allow-indirect-conversion

Show all possible indirect conversions (labelled as intermediate)

--version Show version

--conversion-graph [{cytoscape,cytoscape-all}]

Bioconvert contains tens of converters whose list is available as follows:

bioconvert --help

Each conversion has its own sub-command and dedicated help. For instance:

bioconvert fastq2fasta --help

Because the subcommand contains the format, extensions are not important

for the conversion itself. This would convert the test.txt file (fastq

format) into a fasta file:

bioconvert fastq2fasta test.txt test.fasta

If you use known extensions, the converter may be omitted::

bioconvert test.fastq test.fasta

Users must ensure that their input format files are properly formatted.

If there is a conversion from A to B and another for B to C, you can also

perform indirect conversion using -a argument (experimental). This command

shows all possible indirect conversions:

bioconvert --help -a

Please visit http://bioconvert.readthedocs.org for more information about the

project or formats available. Would you wish to help, please join our open

source collaborative project at https://github/bioconvert/bioconvert

各サブコマンドのhelpも用意されている。fastq2fastaなら

> bioconvert fastq2fasta --help

$ bioconvert fastq2fasta --help

usage: bioconvert fastq2fasta [-h] [-f] [-v {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [--raise-exception] [-X] [-b] [-N BENCHMARK_N] [-T BENCHMARK_TAG] [-I] [--benchmark-mode BENCHMARK_MODE] [-M BENCHMARK_METHODS [BENCHMARK_METHODS ...]] [-a] [-e EXTRA_ARGUMENTS]

[-m [{awk,bioconvert,mappy,mawk,perl,readfq,sed,seqkit,seqtk}]] [-s] [-t THREADS]

[input_file] [output_file]

Convert file from '('FASTQ',)' to '('FASTA',)' format. See bioconvert.readthedocs.io for details

positional arguments:

input_file The path to the file to convert. (default: None)

output_file The path where the result will be stored. (default: None)

options:

-h, --help show this help message and exit

-f, --force if outfile exists, it is overwritten with this option (default: False)

-v {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --verbosity {DEBUG,INFO,WARNING,ERROR,CRITICAL}

Set the outpout verbosity. (default: ERROR)

--raise-exception Let exception ending the execution be raised and displayed (default: False)

-X, --batch Allow conversion of a set of files using wildcards. You must use quotes to escape the wildcards. For instance: --batch 'test*fastq' (default: False)

-b, --benchmark Running all available methods (default: False)

-N BENCHMARK_N, --benchmark-N BENCHMARK_N

Number of trials for each methods (default: 5)

-T BENCHMARK_TAG, --benchmark-tag BENCHMARK_TAG

Save results (json and image) named after this tag. You may include sub directories (default: bioconvert)

-I, --benchmark-save-image

Save results as an image (using the same tag as from --benchmark-tag) (default: False)

--benchmark-mode BENCHMARK_MODE

Set the mode of the benchmark, which can be time, CPU or memory. Defaults to time) (default: time)

-M BENCHMARK_METHODS [BENCHMARK_METHODS ...], --benchmark-methods BENCHMARK_METHODS [BENCHMARK_METHODS ...]

Methods to include. Provide list as space-separated method names. Use -s to get the full list. (default: all)

-a, --allow-indirect-conversion

Allow to chain converter when direct conversion is absent (default: False)

-e EXTRA_ARGUMENTS, --extra-arguments EXTRA_ARGUMENTS

Any arguments accepted by the method's tool (default: )

-m [{awk,bioconvert,mappy,mawk,perl,readfq,sed,seqkit,seqtk}], --method [{awk,bioconvert,mappy,mawk,perl,readfq,sed,seqkit,seqtk}]

The method to use to do the conversion. (default: bioconvert)

-s, --show-methods A converter may have several methods (default: False)

-t THREADS, --threads THREADS

threads to be used (default: 4)

Bioconvert is an open source collaborative project. Please feel free to join us at https://github/biokit/bioconvert

実行方法

１、基本的な使用法。ほとんどの場合、Bioconvert はサブコマンド名と入力と出力のファイル名だけ指定する。

fastqをfastaに変換する。

bioconvert fastq2fasta input.fastq output.fasta

output.fastaが出力される。

出力を指定しない時も標準出力はされず自動でファイルに書き出される。

#input.fastaが保存される
bioconvert fastq2fasta input.fastq

このように、どのようなフォーマット間の変換をするかはサブコマンドで指定する。fastq2fastaならfastqをfastaに変換する（from fastq to (2) fasta）。サブコマンドは非常に多くの種類があるが、説明の前にbioconvertのより柔軟な使い方について確認しておく。

２、暗黙の変換。拡張子が変換名と一致すれば、サブコマンドを指定せずに暗黙の変換を行うことが可能。

bioconvert input.fastq output.fasta

拡張子はいくつか想定されるものに対応している。たとえばFASTAフォーマットなら.faや.fasta、.fnaを認識する。

３、圧縮ファイル。入力・出力いずれでも、汎用的な圧縮形式なら自動で認識する。圧縮ファイルを読み込み、圧縮ファイルで書き出す。

bioconvert test.fastq.gz test.fasta
bioconvert test.fastq.gz test.fasta.gz
bioconvert test.fastq.gz test.fasta.bz2

４、圧縮形式のみ変更。フォーマット変換はせずに圧縮形式のみ変換可能。元のファイルは消えない。

bioconvert test.fastq.gz test.fastq.dsrc

５、ワイルドカード。入力の* や ? などのワイルドカードも認識して順次変換可能。出力を指定しないために暗黙の変換はできない。サブコマンドを指定してどんな変換を行うのか明示する。

#fastq => fasta
bioconvert fastq2fasta "*.fastq"

もしくはループで回す（解説）。

６、SRAのダウンロード。サブコマンドsra2fastqを使えば、SRAのデータをダウンロードして、fastq_dumpによりfastq形式に変換して書き出せる。

bioconvert sra2fastq ERR043367

-m [{fastq_dump}] The method to use to do the conversion. (default: fastq_dump)

ペアエンドシークエンシングなら２つのファイルとして保存される。

７、sam <=> bam変換。samtoolsで行うsam => bam変換を行うことが出来る（coordinate sort）。

#暗黙的に変換 sam => bam
bioconvert ERR043367.sam ERR043367.bam

#bam => sam
bioconvert ERR043367.bam ERR043367.bam

#サブコマンドを明示して変換 sam => bam
bioconvert sam2bam ERR043367.sam

-m [{samtools}] The method to use to do the conversion. (default: samtools)
-t threads to be used (default: 4)
-X Allow conversion of a set of files using wildcards. You must use quotes to escape the wildcards. For instance: --batch 'test*fastq' (default: False)

データストリーム処理には対応していないので、他のコマンドと組み合わせるのはあまり良くない。例；マッピングしてbam形式で保存。

minimap2 -a ref.fasta reads.fq | bioconvert sam2bam - out.bam

８、各サブコマンド。順番に見ていく。helpに出るサブコマンド全てを載せている。

ABI =>

abi2fasta abi to-> fasta (1 methods)
abi2fastq abi to-> fastq (1 methods)
abi2qual abi to-> qual (1 methods)

BAM =>

bam2bedgraph bam to-> bedgraph (2 methods)
bam2bigwig bam to-> bigwig (2 methods)
bam2cov bam to-> cov (2 methods)
bam2cram bam to-> cram (1 methods)
bam2fasta bam to-> fasta (1 methods)
bam2fastq bam to-> fastq (2 methods)
bam2json bam to-> json (1 methods)
bam2sam bam to-> sam (4 methods)
bam2tsv bam to-> tsv (2 methods)
bam2wiggle bam to-> wiggle (1 methods)

BCF =>

bcf2vcf bcf to-> vcf (1 methods)
bcf2wiggle bcf to-> wiggle (1 methods)

BED =>

bed2wiggle bed to-> wiggle (1 methods)
bedgraph2bigwig bedgraph to-> bigwig (1 methods)
bedgraph2cov bedgraph to-> cov (1 methods)
bedgraph2wiggle bedgraph to-> wiggle (1 methods)

BIGBED=>

bigbed2bed bigbed to-> bed (1 methods)
bigbed2wiggle bigbed to-> wiggle (1 methods)

BIGWIG =>

bigwig2bedgraph bigwig to-> bedgraph (2 methods)
bigwig2wiggle bigwig to-> wiggle (1 methods)

BED for plink =>

bplink2plink bplink to-> plink (1 methods)
bplink2vcf bplink to-> vcf (1 methods)

BZ2 (bzip2) =>

bz22gz bz2 to-> gz (2 methods)

CLUSTAL =>

clustal2fasta clustal to-> fasta (3 methods)
clustal2nexus clustal to-> nexus (1 methods)
clustal2phylip clustal to-> phylip (2 methods)
clustal2stockholm clustal to-> stockholm (2 methods)

CRAM =>

cram2bam cram to-> bam (1 methods)
cram2fasta cram to-> fasta (1 methods)
cram2fastq cram to-> fastq (1 methods)
cram2sam cram to-> sam (1 methods)

CSV =>

csv2tsv csv to-> tsv (3 methods)
csv2xls csv to-> xls (2 methods)

DSRC =>

dsrc2gz dsrc to-> gz (1 methods)

EMBL =>

embl2fasta embl to-> fasta (2 methods)
embl2genbank embl to-> genbank (2 methods)

FASTA =>

fasta2clustal fasta to-> clustal (3 methods)
fasta2faa fasta to-> faa (1 methods)
fasta2fasta_agp fasta to-> fasta_agp (1 methods)
fasta2fastq fasta to-> fastq (1 methods)
fasta2genbank fasta to-> genbank (3 methods)
fasta2nexus fasta to-> nexus (1 methods)
fasta2phylip fasta to-> phylip (3 methods)
fasta2twobit fasta to-> twobit (1 methods)
fasta_qual2fastq fasta_qual to-> fastq (1 methods)

FastQ (fastq) =>

fastq2fasta fastq to-> fasta (9 methods)
fastq2fasta_qual fastq to-> fasta_qual (1 methods)
fastq2qual fastq to-> qual (1 methods)

GENBANK =>

genbank2embl genbank to-> embl (2 methods)
genbank2fasta genbank to-> fasta (3 methods)
genbank2gff3 genbank to-> gff3 (1 methods)

GFA =>

gfa2fasta gfa to-> fasta (2 methods)

GFF =>

gff22gff3 gff2 to-> gff3 (1 methods)
gff32gff2 gff3 to-> gff2 (1 methods)
gff32gtf gff3 to-> gtf (1 methods)

GZ2 =>

gz2bz2 gz -to-> bz2 (3 methods)
gz2dsrc gz -to-> dsrc (1 methods)

JSON =>

json2yaml json to-> yaml (1 methods)

MAF =>

maf2sam maf to-> sam (1 methods)

NEWICK =>

newick2nexus newick to-> nexus (1 methods)
newick2phyloxml newick to-> phyloxml (1 methods)

NEXUS =>

nexus2clustal nexus to-> clustal (3 methods)
nexus2fasta nexus to-> fasta (3 methods)
nexus2newick nexus to-> newick (2 methods)
nexus2phylip nexus to-> phylip (1 methods)
nexus2phyloxml nexus to-> phyloxml (1 methods)

ODS (.ods) =>

ods2csv ods to-> csv (1 methods)

PDB =>

pdb2faa pdb to-> faa (1 methods)

PHYLIP =>

phylip2clustal phylip to-> clustal (2 methods)
phylip2fasta phylip to-> fasta (3 methods)
phylip2nexus phylip to-> nexus (1 methods)
phylip2stockholm phylip to-> stockholm (2 methods)
phylip2xmfa phylip to-> xmfa (1 methods)

PHYLOXML =>

phyloxml2newick phyloxml to-> newick (1 methods)
phyloxml2nexus phyloxml to-> nexus (1 methods)

PLINK =>

plink2bplink plink to-> bplink (1 methods)
plink2vcf plink to-> vcf (1 methods)

SAM =>

sam2bam sam to-> bam (1 methods)
sam2cram sam to-> cram (1 methods)
sam2paf sam to-> paf (1 methods)

SCF =>

scf2fasta scf to-> fasta (1 methods)
scf2fastq scf to-> fastq (1 methods)

SRA =>

sra2fastq sra to-> fastq (1 methods)

STOCKHOLM =>

stockholm2clustal stockholm to-> clustal (2 methods)
stockholm2phylip stockholm to-> phylip (2 methods)

TSV =>

tsv2csv tsv to-> csv (3 methods)

TWOBIT =>

twobit2fasta twobit to-> fasta (2 methods)

VCF =>

vcf2bcf vcf to-> bcf (1 methods)
vcf2bed vcf to-> bed (1 methods)
vcf2bplink vcf to-> bplink (1 methods)
vcf2plink vcf to-> plink (1 methods)
vcf2wiggle vcf to-> wiggle (1 methods)

WIG =>

wig2bed wig to-> bed (1 methods)

XLS =>

xls2csv xls to-> csv (2 methods)
xlsx2csv xlsx to-> csv (2 methods)

XMFA =>

xmfa2phylip xmfa to-> phylip (1 methods)

YAML =>

yaml2json yaml to-> json (1 methods)

９、間接変換

さらに、A => B変換を経てB =>C変換をしたい場合、-a引数（現在 experimental）を使って間接変換を行うこともできる。 "-a Allow to chain converter when direct conversion is absent (default: False)"

bioconvert --help -aで表示されるヘルプにおいて、"intermediate"が付いているのが間接変換を行うコマンドになる。

sub-command help

abi2fasta abi to-> fasta (1 methods)

abi2fastq abi to-> fastq (1 methods)

abi2qual abi to-> qual (1 methods)

abi2clustal abi to~> clustal (w/ 1 intermediate)

abi2faa abi to~> faa (w/ 1 intermediate)

abi2fasta_agp abi to~> fasta_agp (w/ 1 intermediate)

abi2genbank abi to~> genbank (w/ 1 intermediate)

abi2nexus abi to~> nexus (w/ 1 intermediate)

abi2phylip abi to~> phylip (w/ 1 intermediate)

abi2twobit abi to~> twobit (w/ 1 intermediate)

abi2fasta_qual abi to~> fasta_qual (w/ 1 intermediate)

abi2stockholm abi to~> stockholm (w/ 2 intermediates)

abi2embl abi to~> embl (w/ 2 intermediates)

abi2gff3 abi to~> gff3 (w/ 2 intermediates)

abi2newick abi to~> newick (w/ 2 intermediates)

abi2phyloxml abi to~> phyloxml (w/ 2 intermediates)

abi2xmfa abi to~> xmfa (w/ 2 intermediates)

abi2gff2 abi to~> gff2 (w/ 3 intermediates)

abi2gtf abi to~> gtf (w/ 3 intermediates)

bam2bedgraph bam to-> bedgraph (2 methods)

bam2bigwig bam to-> bigwig (2 methods)

bam2cov bam to-> cov (2 methods)

bam2cram bam to-> cram (1 methods)

bam2fasta bam to-> fasta (1 methods)

bam2fastq bam to-> fastq (2 methods)

bam2json bam to-> json (1 methods)

bam2sam bam to-> sam (4 methods)

bam2tsv bam to-> tsv (2 methods)

bam2wiggle bam to-> wiggle (1 methods)

bam2clustal bam to~> clustal (w/ 1 intermediate)

bam2faa bam to~> faa (w/ 1 intermediate)

bam2fasta_agp bam to~> fasta_agp (w/ 1 intermediate)

bam2genbank bam to~> genbank (w/ 1 intermediate)

bam2nexus bam to~> nexus (w/ 1 intermediate)

bam2phylip bam to~> phylip (w/ 1 intermediate)

bam2twobit bam to~> twobit (w/ 1 intermediate)

bam2fasta_qual bam to~> fasta_qual (w/ 1 intermediate)

bam2qual bam to~> qual (w/ 1 intermediate)

bam2yaml bam to~> yaml (w/ 1 intermediate)

bam2paf bam to~> paf (w/ 1 intermediate)

bam2csv bam to~> csv (w/ 1 intermediate)

bam2stockholm bam to~> stockholm (w/ 2 intermediates)

bam2embl bam to~> embl (w/ 2 intermediates)

bam2gff3 bam to~> gff3 (w/ 2 intermediates)

bam2newick bam to~> newick (w/ 2 intermediates)

bam2phyloxml bam to~> phyloxml (w/ 2 intermediates)

bam2xmfa bam to~> xmfa (w/ 2 intermediates)

bam2xls bam to~> xls (w/ 2 intermediates)

bam2gff2 bam to~> gff2 (w/ 3 intermediates)

bam2gtf bam to~> gtf (w/ 3 intermediates)

bcf2vcf bcf to-> vcf (1 methods)

bcf2wiggle bcf to-> wiggle (1 methods)

bcf2bed bcf to~> bed (w/ 1 intermediate)

bcf2bplink bcf to~> bplink (w/ 1 intermediate)

bcf2plink bcf to~> plink (w/ 1 intermediate)

bed2wiggle bed to-> wiggle (1 methods)

bedgraph2bigwig bedgraph to-> bigwig (1 methods)

bedgraph2cov bedgraph to-> cov (1 methods)

bedgraph2wiggle bedgraph to-> wiggle (1 methods)

bigbed2bed bigbed to-> bed (1 methods)

bigbed2wiggle bigbed to-> wiggle (1 methods)

bigwig2bedgraph bigwig to-> bedgraph (2 methods)

bigwig2wiggle bigwig to-> wiggle (1 methods)

bigwig2cov bigwig to~> cov (w/ 1 intermediate)

bplink2plink bplink to-> plink (1 methods)

bplink2vcf bplink to-> vcf (1 methods)

bplink2bcf bplink to~> bcf (w/ 1 intermediate)

bplink2bed bplink to~> bed (w/ 1 intermediate)

bplink2wiggle bplink to~> wiggle (w/ 1 intermediate)

bz22gz bz2 to-> gz (2 methods)

bz22dsrc bz2 to~> dsrc (w/ 1 intermediate)

clustal2fasta clustal to-> fasta (3 methods)

clustal2nexus clustal to-> nexus (1 methods)

clustal2phylip clustal to-> phylip (2 methods)

clustal2stockholm clustal to-> stockholm (2 methods)

clustal2faa clustal to~> faa (w/ 1 intermediate)

clustal2fasta_agp clustal to~> fasta_agp (w/ 1 intermediate)

clustal2fastq clustal to~> fastq (w/ 1 intermediate)

clustal2genbank clustal to~> genbank (w/ 1 intermediate)

clustal2twobit clustal to~> twobit (w/ 1 intermediate)

clustal2newick clustal to~> newick (w/ 1 intermediate)

clustal2phyloxml clustal to~> phyloxml (w/ 1 intermediate)

clustal2xmfa clustal to~> xmfa (w/ 1 intermediate)

clustal2fasta_qual clustal to~> fasta_qual (w/ 2 intermediates)

clustal2qual clustal to~> qual (w/ 2 intermediates)

clustal2embl clustal to~> embl (w/ 2 intermediates)

clustal2gff3 clustal to~> gff3 (w/ 2 intermediates)

clustal2gff2 clustal to~> gff2 (w/ 3 intermediates)

clustal2gtf clustal to~> gtf (w/ 3 intermediates)

cram2bam cram to-> bam (1 methods)

cram2fasta cram to-> fasta (1 methods)

cram2fastq cram to-> fastq (1 methods)

cram2sam cram to-> sam (1 methods)

cram2bedgraph cram to~> bedgraph (w/ 1 intermediate)

cram2bigwig cram to~> bigwig (w/ 1 intermediate)

cram2cov cram to~> cov (w/ 1 intermediate)

cram2json cram to~> json (w/ 1 intermediate)

cram2tsv cram to~> tsv (w/ 1 intermediate)

cram2wiggle cram to~> wiggle (w/ 1 intermediate)

cram2clustal cram to~> clustal (w/ 1 intermediate)

cram2faa cram to~> faa (w/ 1 intermediate)

cram2fasta_agp cram to~> fasta_agp (w/ 1 intermediate)

cram2genbank cram to~> genbank (w/ 1 intermediate)

cram2nexus cram to~> nexus (w/ 1 intermediate)

cram2phylip cram to~> phylip (w/ 1 intermediate)

cram2twobit cram to~> twobit (w/ 1 intermediate)

cram2fasta_qual cram to~> fasta_qual (w/ 1 intermediate)

cram2qual cram to~> qual (w/ 1 intermediate)

cram2paf cram to~> paf (w/ 1 intermediate)

cram2yaml cram to~> yaml (w/ 2 intermediates)

cram2csv cram to~> csv (w/ 2 intermediates)

cram2stockholm cram to~> stockholm (w/ 2 intermediates)

cram2embl cram to~> embl (w/ 2 intermediates)

cram2gff3 cram to~> gff3 (w/ 2 intermediates)

cram2newick cram to~> newick (w/ 2 intermediates)

cram2phyloxml cram to~> phyloxml (w/ 2 intermediates)

cram2xmfa cram to~> xmfa (w/ 2 intermediates)

cram2xls cram to~> xls (w/ 3 intermediates)

cram2gff2 cram to~> gff2 (w/ 3 intermediates)

cram2gtf cram to~> gtf (w/ 3 intermediates)

csv2tsv csv to-> tsv (3 methods)

csv2xls csv to-> xls (2 methods)

dsrc2gz dsrc to-> gz (1 methods)

dsrc2bz2 dsrc to~> bz2 (w/ 1 intermediate)

embl2fasta embl to-> fasta (2 methods)

embl2genbank embl to-> genbank (2 methods)

embl2clustal embl to~> clustal (w/ 1 intermediate)

embl2faa embl to~> faa (w/ 1 intermediate)

embl2fasta_agp embl to~> fasta_agp (w/ 1 intermediate)

embl2fastq embl to~> fastq (w/ 1 intermediate)

embl2nexus embl to~> nexus (w/ 1 intermediate)

embl2phylip embl to~> phylip (w/ 1 intermediate)

embl2twobit embl to~> twobit (w/ 1 intermediate)

embl2gff3 embl to~> gff3 (w/ 1 intermediate)

embl2stockholm embl to~> stockholm (w/ 2 intermediates)

embl2fasta_qual embl to~> fasta_qual (w/ 2 intermediates)

embl2qual embl to~> qual (w/ 2 intermediates)

embl2newick embl to~> newick (w/ 2 intermediates)

embl2phyloxml embl to~> phyloxml (w/ 2 intermediates)

embl2xmfa embl to~> xmfa (w/ 2 intermediates)

embl2gff2 embl to~> gff2 (w/ 2 intermediates)

embl2gtf embl to~> gtf (w/ 2 intermediates)

fasta2clustal fasta to-> clustal (3 methods)

fasta2faa fasta to-> faa (1 methods)

fasta2fasta_agp fasta to-> fasta_agp (1 methods)

fasta2fastq fasta to-> fastq (1 methods)

fasta2genbank fasta to-> genbank (3 methods)

fasta2nexus fasta to-> nexus (1 methods)

fasta2phylip fasta to-> phylip (3 methods)

fasta2twobit fasta to-> twobit (1 methods)

fasta2stockholm fasta to~> stockholm (w/ 1 intermediate)

fasta2fasta_qual fasta to~> fasta_qual (w/ 1 intermediate)

fasta2qual fasta to~> qual (w/ 1 intermediate)

fasta2embl fasta to~> embl (w/ 1 intermediate)

fasta2gff3 fasta to~> gff3 (w/ 1 intermediate)

fasta2newick fasta to~> newick (w/ 1 intermediate)

fasta2phyloxml fasta to~> phyloxml (w/ 1 intermediate)

fasta2xmfa fasta to~> xmfa (w/ 1 intermediate)

fasta2gff2 fasta to~> gff2 (w/ 2 intermediates)

fasta2gtf fasta to~> gtf (w/ 2 intermediates)

fasta_qual2fastq fasta_qual to-> fastq (1 methods)

fasta_qual2fasta fasta_qual to~> fasta (w/ 1 intermediate)

fasta_qual2qual fasta_qual to~> qual (w/ 1 intermediate)

fasta_qual2clustal fasta_qual to~> clustal (w/ 2 intermediates)

fasta_qual2faa fasta_qual to~> faa (w/ 2 intermediates)

fasta_qual2fasta_agp

fasta_qual to~> fasta_agp (w/ 2 intermediates)

fasta_qual2genbank fasta_qual to~> genbank (w/ 2 intermediates)

fasta_qual2nexus fasta_qual to~> nexus (w/ 2 intermediates)

fasta_qual2phylip fasta_qual to~> phylip (w/ 2 intermediates)

fasta_qual2twobit fasta_qual to~> twobit (w/ 2 intermediates)

fasta_qual2stockholm

fasta_qual to~> stockholm (w/ 3 intermediates)

fasta_qual2embl fasta_qual to~> embl (w/ 3 intermediates)

fasta_qual2gff3 fasta_qual to~> gff3 (w/ 3 intermediates)

fasta_qual2newick fasta_qual to~> newick (w/ 3 intermediates)

fasta_qual2phyloxml

fasta_qual to~> phyloxml (w/ 3 intermediates)

fasta_qual2xmfa fasta_qual to~> xmfa (w/ 3 intermediates)

fasta_qual2gff2 fasta_qual to~> gff2 (w/ 4 intermediates)

fasta_qual2gtf fasta_qual to~> gtf (w/ 4 intermediates)

fastq2fasta fastq to-> fasta (9 methods)

fastq2fasta_qual fastq to-> fasta_qual (1 methods)

fastq2qual fastq to-> qual (1 methods)

fastq2clustal fastq to~> clustal (w/ 1 intermediate)

fastq2faa fastq to~> faa (w/ 1 intermediate)

fastq2fasta_agp fastq to~> fasta_agp (w/ 1 intermediate)

fastq2genbank fastq to~> genbank (w/ 1 intermediate)

fastq2nexus fastq to~> nexus (w/ 1 intermediate)

fastq2phylip fastq to~> phylip (w/ 1 intermediate)

fastq2twobit fastq to~> twobit (w/ 1 intermediate)

fastq2stockholm fastq to~> stockholm (w/ 2 intermediates)

fastq2embl fastq to~> embl (w/ 2 intermediates)

fastq2gff3 fastq to~> gff3 (w/ 2 intermediates)

fastq2newick fastq to~> newick (w/ 2 intermediates)

fastq2phyloxml fastq to~> phyloxml (w/ 2 intermediates)

fastq2xmfa fastq to~> xmfa (w/ 2 intermediates)

fastq2gff2 fastq to~> gff2 (w/ 3 intermediates)

fastq2gtf fastq to~> gtf (w/ 3 intermediates)

genbank2embl genbank to-> embl (2 methods)

genbank2fasta genbank to-> fasta (3 methods)

genbank2gff3 genbank to-> gff3 (1 methods)

genbank2clustal genbank to~> clustal (w/ 1 intermediate)

genbank2faa genbank to~> faa (w/ 1 intermediate)

genbank2fasta_agp genbank to~> fasta_agp (w/ 1 intermediate)

genbank2fastq genbank to~> fastq (w/ 1 intermediate)

genbank2nexus genbank to~> nexus (w/ 1 intermediate)

genbank2phylip genbank to~> phylip (w/ 1 intermediate)

genbank2twobit genbank to~> twobit (w/ 1 intermediate)

genbank2gff2 genbank to~> gff2 (w/ 1 intermediate)

genbank2gtf genbank to~> gtf (w/ 1 intermediate)

genbank2stockholm genbank to~> stockholm (w/ 2 intermediates)

genbank2fasta_qual genbank to~> fasta_qual (w/ 2 intermediates)

genbank2qual genbank to~> qual (w/ 2 intermediates)

genbank2newick genbank to~> newick (w/ 2 intermediates)

genbank2phyloxml genbank to~> phyloxml (w/ 2 intermediates)

genbank2xmfa genbank to~> xmfa (w/ 2 intermediates)

gfa2fasta gfa to-> fasta (2 methods)

gfa2clustal gfa to~> clustal (w/ 1 intermediate)

gfa2faa gfa to~> faa (w/ 1 intermediate)

gfa2fasta_agp gfa to~> fasta_agp (w/ 1 intermediate)

gfa2fastq gfa to~> fastq (w/ 1 intermediate)

gfa2genbank gfa to~> genbank (w/ 1 intermediate)

gfa2nexus gfa to~> nexus (w/ 1 intermediate)

gfa2phylip gfa to~> phylip (w/ 1 intermediate)

gfa2twobit gfa to~> twobit (w/ 1 intermediate)

gfa2stockholm gfa to~> stockholm (w/ 2 intermediates)

gfa2fasta_qual gfa to~> fasta_qual (w/ 2 intermediates)

gfa2qual gfa to~> qual (w/ 2 intermediates)

gfa2embl gfa to~> embl (w/ 2 intermediates)

gfa2gff3 gfa to~> gff3 (w/ 2 intermediates)

gfa2newick gfa to~> newick (w/ 2 intermediates)

gfa2phyloxml gfa to~> phyloxml (w/ 2 intermediates)

gfa2xmfa gfa to~> xmfa (w/ 2 intermediates)

gfa2gff2 gfa to~> gff2 (w/ 3 intermediates)

gfa2gtf gfa to~> gtf (w/ 3 intermediates)

gff22gff3 gff2 to-> gff3 (1 methods)

gff22gtf gff2 to~> gtf (w/ 1 intermediate)

gff32gff2 gff3 to-> gff2 (1 methods)

gff32gtf gff3 to-> gtf (1 methods)

gz2bz2 gz -to-> bz2 (3 methods)

gz2dsrc gz -to-> dsrc (1 methods)

json2yaml json to-> yaml (1 methods)

maf2sam maf to-> sam (1 methods)

maf2bam maf to~> bam (w/ 1 intermediate)

maf2cram maf to~> cram (w/ 1 intermediate)

maf2paf maf to~> paf (w/ 1 intermediate)

maf2bedgraph maf to~> bedgraph (w/ 2 intermediates)

maf2bigwig maf to~> bigwig (w/ 2 intermediates)

maf2cov maf to~> cov (w/ 2 intermediates)

maf2fasta maf to~> fasta (w/ 2 intermediates)

maf2fastq maf to~> fastq (w/ 2 intermediates)

maf2json maf to~> json (w/ 2 intermediates)

maf2tsv maf to~> tsv (w/ 2 intermediates)

maf2wiggle maf to~> wiggle (w/ 2 intermediates)

maf2clustal maf to~> clustal (w/ 3 intermediates)

maf2faa maf to~> faa (w/ 3 intermediates)

maf2fasta_agp maf to~> fasta_agp (w/ 3 intermediates)

maf2genbank maf to~> genbank (w/ 3 intermediates)

maf2nexus maf to~> nexus (w/ 3 intermediates)

maf2phylip maf to~> phylip (w/ 3 intermediates)

maf2twobit maf to~> twobit (w/ 3 intermediates)

maf2fasta_qual maf to~> fasta_qual (w/ 3 intermediates)

maf2qual maf to~> qual (w/ 3 intermediates)

maf2yaml maf to~> yaml (w/ 3 intermediates)

maf2csv maf to~> csv (w/ 3 intermediates)

maf2stockholm maf to~> stockholm (w/ 4 intermediates)

maf2embl maf to~> embl (w/ 4 intermediates)

maf2gff3 maf to~> gff3 (w/ 4 intermediates)

maf2newick maf to~> newick (w/ 4 intermediates)

maf2phyloxml maf to~> phyloxml (w/ 4 intermediates)

maf2xmfa maf to~> xmfa (w/ 4 intermediates)

maf2xls maf to~> xls (w/ 4 intermediates)

maf2gff2 maf to~> gff2 (w/ 5 intermediates)

maf2gtf maf to~> gtf (w/ 5 intermediates)

newick2nexus newick to-> nexus (1 methods)

newick2phyloxml newick to-> phyloxml (1 methods)

newick2clustal newick to~> clustal (w/ 1 intermediate)

newick2fasta newick to~> fasta (w/ 1 intermediate)

newick2phylip newick to~> phylip (w/ 1 intermediate)

newick2stockholm newick to~> stockholm (w/ 2 intermediates)

newick2faa newick to~> faa (w/ 2 intermediates)

newick2fasta_agp newick to~> fasta_agp (w/ 2 intermediates)

newick2fastq newick to~> fastq (w/ 2 intermediates)

newick2genbank newick to~> genbank (w/ 2 intermediates)

newick2twobit newick to~> twobit (w/ 2 intermediates)

newick2xmfa newick to~> xmfa (w/ 2 intermediates)

newick2fasta_qual newick to~> fasta_qual (w/ 3 intermediates)

newick2qual newick to~> qual (w/ 3 intermediates)

newick2embl newick to~> embl (w/ 3 intermediates)

newick2gff3 newick to~> gff3 (w/ 3 intermediates)

newick2gff2 newick to~> gff2 (w/ 4 intermediates)

newick2gtf newick to~> gtf (w/ 4 intermediates)

nexus2clustal nexus to-> clustal (3 methods)

nexus2fasta nexus to-> fasta (3 methods)

nexus2newick nexus to-> newick (2 methods)

nexus2phylip nexus to-> phylip (1 methods)

nexus2phyloxml nexus to-> phyloxml (1 methods)

nexus2stockholm nexus to~> stockholm (w/ 1 intermediate)

nexus2faa nexus to~> faa (w/ 1 intermediate)

nexus2fasta_agp nexus to~> fasta_agp (w/ 1 intermediate)

nexus2fastq nexus to~> fastq (w/ 1 intermediate)

nexus2genbank nexus to~> genbank (w/ 1 intermediate)

nexus2twobit nexus to~> twobit (w/ 1 intermediate)

nexus2xmfa nexus to~> xmfa (w/ 1 intermediate)

nexus2fasta_qual nexus to~> fasta_qual (w/ 2 intermediates)

nexus2qual nexus to~> qual (w/ 2 intermediates)

nexus2embl nexus to~> embl (w/ 2 intermediates)

nexus2gff3 nexus to~> gff3 (w/ 2 intermediates)

nexus2gff2 nexus to~> gff2 (w/ 3 intermediates)

nexus2gtf nexus to~> gtf (w/ 3 intermediates)

ods2csv ods to-> csv (1 methods)

ods2tsv ods to~> tsv (w/ 1 intermediate)

ods2xls ods to~> xls (w/ 1 intermediate)

pdb2faa pdb to-> faa (1 methods)

phylip2clustal phylip to-> clustal (2 methods)

phylip2fasta phylip to-> fasta (3 methods)

phylip2nexus phylip to-> nexus (1 methods)

phylip2stockholm phylip to-> stockholm (2 methods)

phylip2xmfa phylip to-> xmfa (1 methods)

phylip2faa phylip to~> faa (w/ 1 intermediate)

phylip2fasta_agp phylip to~> fasta_agp (w/ 1 intermediate)

phylip2fastq phylip to~> fastq (w/ 1 intermediate)

phylip2genbank phylip to~> genbank (w/ 1 intermediate)

phylip2twobit phylip to~> twobit (w/ 1 intermediate)

phylip2newick phylip to~> newick (w/ 1 intermediate)

phylip2phyloxml phylip to~> phyloxml (w/ 1 intermediate)

phylip2fasta_qual phylip to~> fasta_qual (w/ 2 intermediates)

phylip2qual phylip to~> qual (w/ 2 intermediates)

phylip2embl phylip to~> embl (w/ 2 intermediates)

phylip2gff3 phylip to~> gff3 (w/ 2 intermediates)

phylip2gff2 phylip to~> gff2 (w/ 3 intermediates)

phylip2gtf phylip to~> gtf (w/ 3 intermediates)

phyloxml2newick phyloxml to-> newick (1 methods)

phyloxml2nexus phyloxml to-> nexus (1 methods)

phyloxml2clustal phyloxml to~> clustal (w/ 1 intermediate)

phyloxml2fasta phyloxml to~> fasta (w/ 1 intermediate)

phyloxml2phylip phyloxml to~> phylip (w/ 1 intermediate)

phyloxml2stockholm phyloxml to~> stockholm (w/ 2 intermediates)

phyloxml2faa phyloxml to~> faa (w/ 2 intermediates)

phyloxml2fasta_agp phyloxml to~> fasta_agp (w/ 2 intermediates)

phyloxml2fastq phyloxml to~> fastq (w/ 2 intermediates)

phyloxml2genbank phyloxml to~> genbank (w/ 2 intermediates)

phyloxml2twobit phyloxml to~> twobit (w/ 2 intermediates)

phyloxml2xmfa phyloxml to~> xmfa (w/ 2 intermediates)

phyloxml2fasta_qual

phyloxml to~> fasta_qual (w/ 3 intermediates)

phyloxml2qual phyloxml to~> qual (w/ 3 intermediates)

phyloxml2embl phyloxml to~> embl (w/ 3 intermediates)

phyloxml2gff3 phyloxml to~> gff3 (w/ 3 intermediates)

phyloxml2gff2 phyloxml to~> gff2 (w/ 4 intermediates)

phyloxml2gtf phyloxml to~> gtf (w/ 4 intermediates)

plink2bplink plink to-> bplink (1 methods)

plink2vcf plink to-> vcf (1 methods)

plink2bcf plink to~> bcf (w/ 1 intermediate)

plink2bed plink to~> bed (w/ 1 intermediate)

plink2wiggle plink to~> wiggle (w/ 1 intermediate)

sam2bam sam to-> bam (1 methods)

sam2cram sam to-> cram (1 methods)

sam2paf sam to-> paf (1 methods)

sam2bedgraph sam to~> bedgraph (w/ 1 intermediate)

sam2bigwig sam to~> bigwig (w/ 1 intermediate)

sam2cov sam to~> cov (w/ 1 intermediate)

sam2fasta sam to~> fasta (w/ 1 intermediate)

sam2fastq sam to~> fastq (w/ 1 intermediate)

sam2json sam to~> json (w/ 1 intermediate)

sam2tsv sam to~> tsv (w/ 1 intermediate)

sam2wiggle sam to~> wiggle (w/ 1 intermediate)

sam2clustal sam to~> clustal (w/ 2 intermediates)

sam2faa sam to~> faa (w/ 2 intermediates)

sam2fasta_agp sam to~> fasta_agp (w/ 2 intermediates)

sam2genbank sam to~> genbank (w/ 2 intermediates)

sam2nexus sam to~> nexus (w/ 2 intermediates)

sam2phylip sam to~> phylip (w/ 2 intermediates)

sam2twobit sam to~> twobit (w/ 2 intermediates)

sam2fasta_qual sam to~> fasta_qual (w/ 2 intermediates)

sam2qual sam to~> qual (w/ 2 intermediates)

sam2yaml sam to~> yaml (w/ 2 intermediates)

sam2csv sam to~> csv (w/ 2 intermediates)

sam2stockholm sam to~> stockholm (w/ 3 intermediates)

sam2embl sam to~> embl (w/ 3 intermediates)

sam2gff3 sam to~> gff3 (w/ 3 intermediates)

sam2newick sam to~> newick (w/ 3 intermediates)

sam2phyloxml sam to~> phyloxml (w/ 3 intermediates)

sam2xmfa sam to~> xmfa (w/ 3 intermediates)

sam2xls sam to~> xls (w/ 3 intermediates)

sam2gff2 sam to~> gff2 (w/ 4 intermediates)

sam2gtf sam to~> gtf (w/ 4 intermediates)

scf2fasta scf to-> fasta (1 methods)

scf2fastq scf to-> fastq (1 methods)

scf2clustal scf to~> clustal (w/ 1 intermediate)

scf2faa scf to~> faa (w/ 1 intermediate)

scf2fasta_agp scf to~> fasta_agp (w/ 1 intermediate)

scf2genbank scf to~> genbank (w/ 1 intermediate)

scf2nexus scf to~> nexus (w/ 1 intermediate)

scf2phylip scf to~> phylip (w/ 1 intermediate)

scf2twobit scf to~> twobit (w/ 1 intermediate)

scf2fasta_qual scf to~> fasta_qual (w/ 1 intermediate)

scf2qual scf to~> qual (w/ 1 intermediate)

scf2stockholm scf to~> stockholm (w/ 2 intermediates)

scf2embl scf to~> embl (w/ 2 intermediates)

scf2gff3 scf to~> gff3 (w/ 2 intermediates)

scf2newick scf to~> newick (w/ 2 intermediates)

scf2phyloxml scf to~> phyloxml (w/ 2 intermediates)

scf2xmfa scf to~> xmfa (w/ 2 intermediates)

scf2gff2 scf to~> gff2 (w/ 3 intermediates)

scf2gtf scf to~> gtf (w/ 3 intermediates)

sra2fastq sra to-> fastq (1 methods)

sra2fasta sra to~> fasta (w/ 1 intermediate)

sra2fasta_qual sra to~> fasta_qual (w/ 1 intermediate)

sra2qual sra to~> qual (w/ 1 intermediate)

sra2clustal sra to~> clustal (w/ 2 intermediates)

sra2faa sra to~> faa (w/ 2 intermediates)

sra2fasta_agp sra to~> fasta_agp (w/ 2 intermediates)

sra2genbank sra to~> genbank (w/ 2 intermediates)

sra2nexus sra to~> nexus (w/ 2 intermediates)

sra2phylip sra to~> phylip (w/ 2 intermediates)

sra2twobit sra to~> twobit (w/ 2 intermediates)

sra2stockholm sra to~> stockholm (w/ 3 intermediates)

sra2embl sra to~> embl (w/ 3 intermediates)

sra2gff3 sra to~> gff3 (w/ 3 intermediates)

sra2newick sra to~> newick (w/ 3 intermediates)

sra2phyloxml sra to~> phyloxml (w/ 3 intermediates)

sra2xmfa sra to~> xmfa (w/ 3 intermediates)

sra2gff2 sra to~> gff2 (w/ 4 intermediates)

sra2gtf sra to~> gtf (w/ 4 intermediates)

stockholm2clustal stockholm to-> clustal (2 methods)

stockholm2phylip stockholm to-> phylip (2 methods)

stockholm2fasta stockholm to~> fasta (w/ 1 intermediate)

stockholm2nexus stockholm to~> nexus (w/ 1 intermediate)

stockholm2xmfa stockholm to~> xmfa (w/ 1 intermediate)

stockholm2faa stockholm to~> faa (w/ 2 intermediates)

stockholm2fasta_agp

stockholm to~> fasta_agp (w/ 2 intermediates)

stockholm2fastq stockholm to~> fastq (w/ 2 intermediates)

stockholm2genbank stockholm to~> genbank (w/ 2 intermediates)

stockholm2twobit stockholm to~> twobit (w/ 2 intermediates)

stockholm2newick stockholm to~> newick (w/ 2 intermediates)

stockholm2phyloxml stockholm to~> phyloxml (w/ 2 intermediates)

stockholm2fasta_qual

stockholm to~> fasta_qual (w/ 3 intermediates)

stockholm2qual stockholm to~> qual (w/ 3 intermediates)

stockholm2embl stockholm to~> embl (w/ 3 intermediates)

stockholm2gff3 stockholm to~> gff3 (w/ 3 intermediates)

stockholm2gff2 stockholm to~> gff2 (w/ 4 intermediates)

stockholm2gtf stockholm to~> gtf (w/ 4 intermediates)

tsv2csv tsv to-> csv (3 methods)

tsv2xls tsv to~> xls (w/ 1 intermediate)

twobit2fasta twobit to-> fasta (2 methods)

twobit2clustal twobit to~> clustal (w/ 1 intermediate)

twobit2faa twobit to~> faa (w/ 1 intermediate)

twobit2fasta_agp twobit to~> fasta_agp (w/ 1 intermediate)

twobit2fastq twobit to~> fastq (w/ 1 intermediate)

twobit2genbank twobit to~> genbank (w/ 1 intermediate)

twobit2nexus twobit to~> nexus (w/ 1 intermediate)

twobit2phylip twobit to~> phylip (w/ 1 intermediate)

twobit2stockholm twobit to~> stockholm (w/ 2 intermediates)

twobit2fasta_qual twobit to~> fasta_qual (w/ 2 intermediates)

twobit2qual twobit to~> qual (w/ 2 intermediates)

twobit2embl twobit to~> embl (w/ 2 intermediates)

twobit2gff3 twobit to~> gff3 (w/ 2 intermediates)

twobit2newick twobit to~> newick (w/ 2 intermediates)

twobit2phyloxml twobit to~> phyloxml (w/ 2 intermediates)

twobit2xmfa twobit to~> xmfa (w/ 2 intermediates)

twobit2gff2 twobit to~> gff2 (w/ 3 intermediates)

twobit2gtf twobit to~> gtf (w/ 3 intermediates)

vcf2bcf vcf to-> bcf (1 methods)

vcf2bed vcf to-> bed (1 methods)

vcf2bplink vcf to-> bplink (1 methods)

vcf2plink vcf to-> plink (1 methods)

vcf2wiggle vcf to-> wiggle (1 methods)

wig2bed wig to-> bed (1 methods)

wig2wiggle wig to~> wiggle (w/ 1 intermediate)

xls2csv xls to-> csv (2 methods)

xls2tsv xls to~> tsv (w/ 1 intermediate)

xlsx2csv xlsx to-> csv (2 methods)

xlsx2tsv xlsx to~> tsv (w/ 1 intermediate)

xlsx2xls xlsx to~> xls (w/ 1 intermediate)

xmfa2phylip xmfa to-> phylip (1 methods)

xmfa2clustal xmfa to~> clustal (w/ 1 intermediate)

xmfa2fasta xmfa to~> fasta (w/ 1 intermediate)

xmfa2nexus xmfa to~> nexus (w/ 1 intermediate)

xmfa2stockholm xmfa to~> stockholm (w/ 1 intermediate)

xmfa2faa xmfa to~> faa (w/ 2 intermediates)

xmfa2fasta_agp xmfa to~> fasta_agp (w/ 2 intermediates)

xmfa2fastq xmfa to~> fastq (w/ 2 intermediates)

xmfa2genbank xmfa to~> genbank (w/ 2 intermediates)

xmfa2twobit xmfa to~> twobit (w/ 2 intermediates)

xmfa2newick xmfa to~> newick (w/ 2 intermediates)

xmfa2phyloxml xmfa to~> phyloxml (w/ 2 intermediates)

xmfa2fasta_qual xmfa to~> fasta_qual (w/ 3 intermediates)

xmfa2qual xmfa to~> qual (w/ 3 intermediates)

xmfa2embl xmfa to~> embl (w/ 3 intermediates)

xmfa2gff3 xmfa to~> gff3 (w/ 3 intermediates)

xmfa2gff2 xmfa to~> gff2 (w/ 4 intermediates)

xmfa2gtf xmfa to~> gtf (w/ 4 intermediates)

yaml2json yaml to-> json (1 methods)

間接変換では１つ以上の中間ファイルを経てフォーマット変換が行われる。

その他

変換するファイルがたくさんある場合は、Sequanaプロジェクトにsnakemakeパイプラインが用意されており、pip install sequana_bioconvertでインストールできる（解説）。
pythonのコンソール上でも使用できる。
サブコマンドが用意されていても、変換が無理なら実行されない。例えばfasta => clustalフォーマット変換は、fasta形式のMSAを想定しているので、入力ファイル内に配列が１つしか存在しないとかなら実行されない。

引用

BioConvert: a comprehensive format converter for life sciences
Hugo Caro, Sulyvan Dollin, Anne Biton, Bryan Brancotte, Dimitri Desvillechabrol, Yoann Dufresne, Blaise Li, Etienne Kornobis, Frédéric Lemoine, Nicolas Maillet, Amandine Perrin, Nicolas Traut, Bertrand Néron, Thomas Cokelaer

bioRxiv, Posted March 15, 2023