File I/O (skbio.io)

This package provides I/O functionality for skbio.

Supported file formats

For details on what objects are supported by each format, see the associated documentation.

blast6 BLAST+6 format (skbio.io.format.blast6)
blast7 BLAST+7 format (skbio.io.format.blast7)
clustal Clustal format (skbio.io.format.clustal)
embl EMBL format (skbio.io.format.embl)
fasta FASTA/QUAL format (skbio.io.format.fasta)
fastq FASTQ format (skbio.io.format.fastq)
genbank GenBank format (skbio.io.format.genbank)
gff3 GFF3 format (skbio.io.format.gff3)
lsmat Labeled square matrix format (skbio.io.format.lsmat)
newick Newick format (skbio.io.format.newick)
ordination Ordination results format (skbio.io.format.ordination)
phylip PHYLIP multiple sequence alignment format (skbio.io.format.phylip)
qseq QSeq format (skbio.io.format.qseq)
stockholm Stockholm format (skbio.io.format.stockholm)

User functions

write(self, obj, format, into, **kwargs) Write obj as format into a file.
read(self, file[, format, into, verify]) Read file as format into an object.
sniff(self, file, **kwargs) Detect the format of a given file and suggest kwargs for reading.

User exceptions and warnings

FormatIdentificationWarning Warn when the sniffer of a format cannot confirm the format.
ArgumentOverrideWarning Warn when a user provided kwarg differs from a guessed kwarg.
UnrecognizedFormatError Raised when a file’s format is unknown, ambiguous, or unidentifiable.
IOSourceError Raised when a file source cannot be resolved.
FileFormatError Raised when a file cannot be parsed.
BLAST7FormatError Raised when a blast7 formatted file cannot be parsed.
ClustalFormatError Raised when a clustal formatted file cannot be parsed.
EMBLFormatError Raised when a EMBL formatted file cannot be parsed.
FASTAFormatError Raised when a fasta formatted file cannot be parsed.
FASTQFormatError Raised when a fastq formatted file cannot be parsed.
GenBankFormatError Raised when a genbank formatted file cannot be parsed.
GFF3FormatError Raised when a GFF3 formatted file cannot be parsed.
LSMatFormatError Raised when a lsmat formatted file cannot be parsed.
NewickFormatError Raised when a newick formatted file cannot be parsed.
OrdinationFormatError Raised when an ordination formatted file cannot be parsed.
PhylipFormatError Raised when a phylip formatted file cannot be parsed.
QSeqFormatError Raised when a qseq formatted file cannot be parsed.
QUALFormatError Raised when a qual formatted file cannot be parsed.
StockholmFormatError Raised when a stockholm formatted file cannot be parsed.

Subpackages

registry I/O Registry (skbio.io.registry)
util I/O utils (skbio.io.util)

For developer documentation on extending I/O, see skbio.io.registry.

Introduction to I/O

Reading and writing files (I/O) can be a complicated task:

  • A file format can sometimes be read into more than one in-memory representation (i.e., object). For example, a FASTA file can be read into an skbio.alignment.TabularMSA or skbio.sequence.DNA depending on what operations you’d like to perform on your data.
  • A single object might be writeable to more than one file format. For example, an skbio.alignment.TabularMSA object could be written to FASTA, FASTQ, CLUSTAL, or PHYLIP formats, just to name a few.
  • You might not know the exact file format of your file, but you want to read it into an appropriate object.
  • You might want to read multiple files into a single object, or write an object to multiple files.
  • Instead of reading a file into an object, you might want to stream the file using a generator (e.g., if the file cannot be fully loaded into memory).

To address these issues (and others), scikit-bio provides a simple, powerful interface for dealing with I/O. We accomplish this by using a single I/O registry.

What kinds of files scikit-bio can use

To see a complete list of file-like inputs that can be used for reading, writing, and sniffing, see the documentation for skbio.io.util.open().

Reading files into scikit-bio

There are two ways to read files. The first way is to use the procedural interface:

my_obj = skbio.io.read(file, format='someformat', into=SomeSkbioClass)

The second is to use the object-oriented (OO) interface which is automatically constructed from the procedural interface:

my_obj = SomeSkbioClass.read(file, format='someformat')

For example, to read a newick file using both interfaces you would type:

>>> from skbio import read
>>> from skbio import TreeNode
>>> from io import StringIO
>>> open_filehandle = StringIO('(a, b);')
>>> tree = read(open_filehandle, format='newick', into=TreeNode)
>>> tree
<TreeNode, name: unnamed, internal node count: 0, tips count: 2>

For the OO interface:

>>> open_filehandle = StringIO('(a, b);')
>>> tree = TreeNode.read(open_filehandle, format='newick')
>>> tree
<TreeNode, name: unnamed, internal node count: 0, tips count: 2>

In the case of skbio.io.registry.read() if into is not provided, then a generator will be returned. What the generator yields will depend on what format is being read.

When into is provided, format may be omitted and the registry will use its knowledge of the available formats for the requested class to infer the correct format. This format inference is also available in the OO interface, meaning that format may be omitted there as well.

As an example:

>>> open_filehandle = StringIO('(a, b);')
>>> tree = TreeNode.read(open_filehandle)
>>> tree
<TreeNode, name: unnamed, internal node count: 0, tips count: 2>

We call format inference sniffing, much like the csv.Sniffer class of Python’s standard library. The goal of a sniffer is twofold: to identify if a file is a specific format, and if it is, to provide **kwargs which can be used to better parse the file.

Note

There is a built-in sniffer which results in a useful error message if an empty file is provided as input and the format was omitted.

Writing files from scikit-bio

Just as when reading files, there are two ways to write files.

Procedural Interface:

skbio.io.write(my_obj, format='someformat', into=file)

OO Interface:

my_obj.write(file, format='someformat')

In the procedural interface, format is required. Without it, scikit-bio does not know how you want to serialize an object. OO interfaces define a default format, so it may not be necessary to include it.