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scikit-bio 0.6.3 documentation scikit-bio 0.6.3 documentation
  • Install
  • Learn
  • Documentation
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  • Community
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  • About
    • Input and Output (skbio.io)
    • Biological Sequences (skbio.sequence)
    • Sequence Alignments (skbio.alignment)
    • Trees and Phylogenetics (skbio.tree)
    • Community Diversity (skbio.diversity)
    • Multivariate Statistics (skbio.stats)
    • Biological Embeddings (skbio.embedding)
    • Data Table (skbio.table)
    • Metadata (skbio.metadata)
    • Workflow construction (skbio.workflow)
    • Utilities for Developers (skbio.util)
  • GitHub
  • Twitter
  • Install
  • Learn
  • Documentation
  • Contribute
  • Community
  • Releases
  • About
  • Input and Output (skbio.io)
  • Biological Sequences (skbio.sequence)
  • Sequence Alignments (skbio.alignment)
  • Trees and Phylogenetics (skbio.tree)
  • Community Diversity (skbio.diversity)
  • Multivariate Statistics (skbio.stats)
  • Biological Embeddings (skbio.embedding)
  • Data Table (skbio.table)
  • Metadata (skbio.metadata)
  • Workflow construction (skbio.workflow)
  • Utilities for Developers (skbio.util)
  • GitHub
  • Twitter

Section Navigation

  • Simple binary dissimilarity matrix format (skbio.io.format.binary_dm)
  • BIOM-Format (skbio.io.format.biom)
  • BLAST+6 format (skbio.io.format.blast6)
  • BLAST+7 format (skbio.io.format.blast7)
  • Clustal format (skbio.io.format.clustal)
  • EMBL format (skbio.io.format.embl)
  • Embedding format (skbio.io.format.embed).
  • FASTA/QUAL format (skbio.io.format.fasta)
  • FASTQ format (skbio.io.format.fastq)
  • GenBank format (skbio.io.format.genbank)
  • GFF3 format (skbio.io.format.gff3)
  • Labeled square matrix format (skbio.io.format.lsmat)
  • Newick format (skbio.io.format.newick)
  • Ordination results format (skbio.io.format.ordination)
  • PHYLIP multiple sequence alignment format (skbio.io.format.phylip)
  • QSeq format (skbio.io.format.qseq)
  • Stockholm format (skbio.io.format.stockholm)
  • Taxdump format (skbio.io.format.taxdump)
  • Format Support
  • skbio.io.registry.write
  • skbio.io.registry.read
  • skbio.io.registry.sniff
  • I/O utilities (skbio.io.util)
    • skbio.io.util.open
    • skbio.io.util.open_file
    • skbio.io.util.open_files
  • I/O Registry (skbio.io.registry)
  • Input and Output (skbio.io)
  • I/O utilities (skbio.io.util)

I/O utilities (skbio.io.util)#

This module provides utility functions to deal with files and I/O in general.

Functions#

open(file[, mode, encoding, errors, ...])

Convert input into a filehandle.

open_file(file, **kwargs)

Context manager for skbio.io.util.open.

open_files(files, **kwargs)

Context manager for skbio.io.util.open.

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  • Functions

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