macでインフォマティクス

macでインフォマティクス

HTS (NGS) 関連のインフォマティクス情報についてまとめています。

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

 

 

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:

  {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}

                        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