7. References

• 7.1. Core functions
  • 7.1.1. Base
    • ConvArg
    • ConvBase
      • ConvBase.boxplot_benchmark()
      • ConvBase.compute_benchmark()
      • ConvBase.install_tool()
      • ConvBase.name
    • ConvMeta
    • make_chain()
  • 7.1.2. Benchmark
    • Benchmark
      • Benchmark.plot()
      • Benchmark.run_methods()
    • plot_multi_benchmark_max()
  • 7.1.3. Converter
    • Bioconvert
  • 7.1.4. Decorators
    • compressor()
    • in_gz()
    • make_in_gz_tester()
    • out_compressor()
    • requires()
    • requires_nothing()
  • 7.1.5. Downloader
  • 7.1.6. Extensions
    • AttrDict
      • AttrDict.update()
    • extensions
  • 7.1.7. Graph
    • create_graph()
    • create_graph_for_cytoscape()
  • 7.1.8. Registry
    • Registry
      • Registry.conversion_exists()
      • Registry.conversion_path()
      • Registry.get_all_conversions()
      • Registry.get_conversions()
      • Registry.get_conversions_from_ext()
      • Registry.get_converters_names()
      • Registry.get_ext()
      • Registry.iter_converters()
      • Registry.set_ext()
  • 7.1.9. Utils
    • TempFile
    • Timer
    • generate_outfile_name()
    • get_extension()
    • get_format_from_extension()
    • md5()
• 7.2. Reference converters
  • 7.2.1. Summary
  • 7.2.2. All converters documentation
    • ABI2FASTA
      • ABI2FASTA._default_method
      • ABI2FASTA._method_biopython()
    • ABI2FASTQ
      • ABI2FASTQ._default_method
      • ABI2FASTQ._method_biopython()
    • ABI2QUAL
      • ABI2QUAL._default_method
      • ABI2QUAL._method_biopython()
    • BAM2BEDGRAPH
      • BAM2BEDGRAPH._default_method
      • BAM2BEDGRAPH._method_bedtools()
      • BAM2BEDGRAPH._method_mosdepth()
    • BAM2COV
      • BAM2COV._method_bedtools()
      • BAM2COV._method_samtools()
    • BAM2BIGWIG
      • BAM2BIGWIG._default_method
      • BAM2BIGWIG._method_bamCoverage()
      • BAM2BIGWIG._method_ucsc()
    • BAM2CRAM
      • BAM2CRAM._default_method
      • BAM2CRAM._method_samtools()
    • BAM2FASTA
      • BAM2FASTA._default_method
      • BAM2FASTA._method_samtools()
    • BAM2FASTQ
      • BAM2FASTQ._default_method
      • BAM2FASTQ._method_bedtools()
      • BAM2FASTQ._method_samtools()
    • BAM2JSON
      • BAM2JSON._default_method
      • BAM2JSON._method_bamtools()
    • BAM2SAM
      • BAM2SAM._default_method
      • BAM2SAM._method_pysam()
      • BAM2SAM._method_sambamba()
      • BAM2SAM._method_samtools()
    • BAM2TSV
      • BAM2TSV._default_method
      • BAM2TSV._method_pysam()
      • BAM2TSV._method_samtools()
    • BAM2WIGGLE
      • BAM2WIGGLE._method_wiggletools()
    • BCF2VCF
      • BCF2VCF._method_bcftools()
    • BCF2WIGGLE
      • BCF2WIGGLE._default_method
      • BCF2WIGGLE._method_wiggletools()
    • BED2WIGGLE
      • BED2WIGGLE._method_wiggletools()
    • BEDGRAPH2COV
      • BEDGRAPH2COV._default_method
      • BEDGRAPH2COV._method_python()
    • BEDGRAPH2BIGWIG
      • BEDGRAPH2BIGWIG._default_method
      • BEDGRAPH2BIGWIG._method_ucsc()
    • BEDGRAPH2WIGGLE
      • BEDGRAPH2WIGGLE._default_method
      • BEDGRAPH2WIGGLE._method_wiggletools()
    • BIGBED2WIGGLE
      • BIGBED2WIGGLE._default_method
      • BIGBED2WIGGLE._method_wiggletools()
    • BIGBED2BED
      • BIGBED2BED._default_method
      • BIGBED2BED._method_pybigwig()
    • BIGWIG2BEDGRAPH
      • BIGWIG2BEDGRAPH._default_method
      • BIGWIG2BEDGRAPH._method_pybigwig()
      • BIGWIG2BEDGRAPH._method_ucsc()
    • BIGWIG2WIGGLE
      • BIGWIG2WIGGLE._default_method
      • BIGWIG2WIGGLE._method_wiggletools()
    • BPLINK2PLINK
      • BPLINK2PLINK._default_method
      • BPLINK2PLINK._method_plink()
    • BZ22GZ
      • BZ22GZ._default_method
      • BZ22GZ._method_bz2_gz()
      • BZ22GZ._method_python()
    • CLUSTAL2FASTA
      • CLUSTAL2FASTA._default_method
      • CLUSTAL2FASTA._method_biopython()
      • CLUSTAL2FASTA._method_goalign()
      • CLUSTAL2FASTA._method_squizz()
    • CLUSTAL2PHYLIP
      • CLUSTAL2PHYLIP._default_method
      • CLUSTAL2PHYLIP._method_biopython()
      • CLUSTAL2PHYLIP._method_squizz()
    • CLUSTAL2STOCKHOLM
      • CLUSTAL2STOCKHOLM._default_method
      • CLUSTAL2STOCKHOLM._method_biopython()
      • CLUSTAL2STOCKHOLM._method_squizz()
    • CRAM2BAM
      • CRAM2BAM._default_method
      • CRAM2BAM._method_samtools()
    • CRAM2FASTA
      • CRAM2FASTA._default_method
      • CRAM2FASTA._method_samtools()
    • CRAM2FASTQ
      • CRAM2FASTQ._default_method
      • CRAM2FASTQ._method_samtools()
    • CRAM2SAM
      • CRAM2SAM._default_method
      • CRAM2SAM._method_samtools()
    • CSV2TSV
      • CSV2TSV._default_method
      • CSV2TSV._method_pandas()
      • CSV2TSV._method_python()
      • CSV2TSV._method_python_v2()
    • CSV2XLS
      • CSV2XLS._default_method
      • CSV2XLS._method_pandas()
      • CSV2XLS._method_pyexcel()
    • DSRC2GZ
      • DSRC2GZ._default_method
      • DSRC2GZ._method_dsrcpigz()
    • EMBL2FASTA
      • EMBL2FASTA._default_method
      • EMBL2FASTA._method_biopython()
      • EMBL2FASTA._method_squizz()
    • EMBL2GENBANK
      • EMBL2GENBANK._default_method
      • EMBL2GENBANK._method_biopython()
      • EMBL2GENBANK._method_squizz()
    • FASTA_QUAL2FASTQ
      • FASTA_QUAL2FASTQ._default_method
      • FASTA_QUAL2FASTQ._method_pysam()
    • FASTA2CLUSTAL
      • FASTA2CLUSTAL._default_method
      • FASTA2CLUSTAL._method_biopython()
      • FASTA2CLUSTAL._method_goalign()
      • FASTA2CLUSTAL._method_squizz()
    • FASTA2FAA
      • FASTA2FAA._default_method
      • FASTA2FAA._method_bioconvert()
    • FASTA2FASTQ
      • FASTA2FASTQ._default_method
      • FASTA2FASTQ._method_pysam()
    • FASTA2GENBANK
      • FASTA2GENBANK._default_method
      • FASTA2GENBANK._method_bioconvert()
      • FASTA2GENBANK._method_biopython()
      • FASTA2GENBANK._method_squizz()
    • FASTA2NEXUS
      • FASTA2NEXUS._default_method
      • FASTA2NEXUS._method_goalign()
    • FASTA2PHYLIP
      • FASTA2PHYLIP._default_method
      • FASTA2PHYLIP._method_biopython()
      • FASTA2PHYLIP._method_goalign()
      • FASTA2PHYLIP._method_squizz()
    • FASTA2TWOBIT
      • FASTA2TWOBIT._default_method
      • FASTA2TWOBIT._method_ucsc()
    • FASTQ2FASTA
      • FASTQ2FASTA._default_method
      • FASTQ2FASTA._method_awk()
      • FASTQ2FASTA._method_bioconvert()
      • FASTQ2FASTA._method_mappy()
      • FASTQ2FASTA._method_mawk()
      • FASTQ2FASTA._method_perl()
      • FASTQ2FASTA._method_readfq()
      • FASTQ2FASTA._method_sed()
      • FASTQ2FASTA._method_seqkit()
      • FASTQ2FASTA._method_seqtk()
      • FASTQ2FASTA.just_name()
      • FASTQ2FASTA.unwrap_fasta()
    • GENBANK2EMBL
      • GENBANK2EMBL._default_method
      • GENBANK2EMBL._method_biopython()
      • GENBANK2EMBL._method_squizz()
    • GENBANK2FASTA
      • GENBANK2FASTA._default_method
      • GENBANK2FASTA._method_biopython()
      • GENBANK2FASTA._method_python()
      • GENBANK2FASTA._method_squizz()
    • GENBANK2GFF3
      • GENBANK2GFF3._default_method
      • GENBANK2GFF3._method_biocode()
    • GFF22GFF3
      • GFF22GFF3._default_method
      • GFF22GFF3._method_bioconvert()
    • GFF32GFF2
      • GFF32GFF2._default_method
      • GFF32GFF2._method_bioconvert()
    • GFA2FASTA
      • GFA2FASTA._default_method
      • GFA2FASTA._method_awk()
      • GFA2FASTA._method_python()
    • GZ2BZ2
      • GZ2BZ2._default_method
      • GZ2BZ2._method_gunzip_bzip2()
      • GZ2BZ2._method_pigz_pbzip2()
      • GZ2BZ2._method_python()
    • GZ2DSRC
      • GZ2DSRC._default_method
      • GZ2DSRC._method_pigzdsrc()
    • JSON2YAML
      • JSON2YAML._default_method
      • JSON2YAML._method_yaml()
    • MAF2SAM
      • MAF2SAM._default_method
      • MAF2SAM._method_python()
    • NEWICK2NEXUS
      • NEWICK2NEXUS._default_method
      • NEWICK2NEXUS._method_gotree()
    • NEWICK2PHYLOXML
      • NEWICK2PHYLOXML._default_method
      • NEWICK2PHYLOXML._method_gotree()
    • NEXUS2FASTA
      • NEXUS2FASTA._default_method
      • NEXUS2FASTA._method_biopython()
      • NEXUS2FASTA._method_goalign()
      • NEXUS2FASTA._method_squizz()
    • NEXUS2NEWICK
      • NEXUS2NEWICK._default_method
      • NEXUS2NEWICK._method_biopython()
      • NEXUS2NEWICK._method_gotree()
    • NEXUS2PHYLIP
      • NEXUS2PHYLIP._default_method
      • NEXUS2PHYLIP._method_goalign()
    • NEXUS2PHYLOXML
      • NEXUS2PHYLOXML._default_method
      • NEXUS2PHYLOXML._method_gotree()
    • ODS2CSV
      • ODS2CSV._default_method
      • ODS2CSV._method_pyexcel()
    • PHYLIP2CLUSTAL
      • PHYLIP2CLUSTAL._default_method
      • PHYLIP2CLUSTAL._method_biopython()
      • PHYLIP2CLUSTAL._method_squizz()
    • PHYLIP2FASTA
      • PHYLIP2FASTA._default_method
      • PHYLIP2FASTA._method_biopython()
      • PHYLIP2FASTA._method_goalign()
      • PHYLIP2FASTA._method_squizz()
    • PHYLIP2NEXUS
      • PHYLIP2NEXUS._default_method
      • PHYLIP2NEXUS._method_goalign()
    • PHYLIP2STOCKHOLM
      • PHYLIP2STOCKHOLM._default_method
      • PHYLIP2STOCKHOLM._method_biopython()
      • PHYLIP2STOCKHOLM._method_squizz()
    • PHYLIP2XMFA
      • PHYLIP2XMFA._default_method
      • PHYLIP2XMFA._method_biopython()
    • PHYLOXML2NEWICK
      • PHYLOXML2NEWICK._default_method
      • PHYLOXML2NEWICK._method_gotree()
    • PHYLOXML2NEXUS
      • PHYLOXML2NEXUS._default_method
      • PHYLOXML2NEXUS._method_gotree()
    • PLINK2BPLINK
      • PLINK2BPLINK._default_method
      • PLINK2BPLINK._method_plink()
    • SAM2BAM
      • SAM2BAM._default_method
      • SAM2BAM._method_samtools()
    • SAM2CRAM
      • SAM2CRAM._default_method
      • SAM2CRAM._method_samtools()
    • SAM2PAF
      • SAM2PAF._default_method
      • SAM2PAF._method_python()
    • SCF2FASTA
      • SCF2FASTA._default_method
      • SCF2FASTA._method_python()
    • SCF2FASTQ
      • SCF2FASTQ._default_method
      • SCF2FASTQ._method_python()
    • SRA2FASTQ
      • SRA2FASTQ._default_method
      • SRA2FASTQ._method_fastq_dump()
    • STOCKHOLM2CLUSTAL
      • STOCKHOLM2CLUSTAL._default_method
      • STOCKHOLM2CLUSTAL._method_biopython()
      • STOCKHOLM2CLUSTAL._method_squizz()
    • STOCKHOLM2PHYLIP
      • STOCKHOLM2PHYLIP._default_method
      • STOCKHOLM2PHYLIP._method_biopython()
      • STOCKHOLM2PHYLIP._method_squizz()
    • TSV2CSV
      • TSV2CSV._default_method
      • TSV2CSV._method_pandas()
      • TSV2CSV._method_python()
      • TSV2CSV._method_python_v2()
    • TWOBIT2FASTA
      • TWOBIT2FASTA._default_method
      • TWOBIT2FASTA._method_py2bit()
      • TWOBIT2FASTA._method_ucsc()
    • VCF2BCF
      • VCF2BCF._default_method
      • VCF2BCF._method_bcftools()
    • VCF2BED
      • VCF2BED._default_method
      • VCF2BED._method_awk()
    • VCF2WIGGLE
      • VCF2WIGGLE._default_method
      • VCF2WIGGLE._method_wiggletools()
    • XLS2CSV
      • XLS2CSV._method_pandas()
      • XLS2CSV._method_pyexcel()
    • XLSX2CSV
      • XLSX2CSV._default_method
      • XLSX2CSV._method_pandas()
      • XLSX2CSV._method_pyexcel()
    • XMFA2PHYLIP
      • XMFA2PHYLIP._default_method
      • XMFA2PHYLIP._method_biopython()
    • YAML2JSON
      • YAML2JSON._default_method
      • YAML2JSON._method_python()
      • YAML2JSON.get_json()
• 7.3. IO functions
  • read_from_buffer()
  • MAF
    • MAF.count_insertions()
  • MAFLine