File Formats and Directory Formats

Formats are on-disk representations of semantic types, and are the materialized data/ saved in the payload by the framework when reading and writing artifacts.

QIIME 2 doesn’t have much of an opinion on how data should be represented or stored, so long as it can be represented or stored in an archive.

File Formats

The simplest Formats are the TextFileFormat and the BinaryFileFormat. These formats represent a single file with a fixed on-disk representation.

Validation

Both types of FileFormat support validation hooks — this is (typically) a small bit of code that is run when initially loading a file from an archive - it allows the framework to ensure that the the data contained within the archive at least looks like it’s declared type. This works very well for on-the-fly loading and saving, and goes a long way to preventing corrupt or invalid data from persisting. The one “gotcha” here is that in order to keep things quick, we typically recommend that “minimal” validation occurs over a limited subset of the file (e.g. the first 10 records in a FASTQ file). Because of this, formats allow for multiple levels of sniffing to be defined (currently there are two levels, min and max).

class IntSequenceFormat(TextFileFormat):
    """
    A sequence of integers stored on new lines in a file. Since this is a
    sequence, the integers have an order and repetition of elements is
    allowed. Sequential values must have an inter-value distance other than
    3 to be valid.
    """
    def _validate_n_ints(self, n):
        with self.open() as fh:
            last_val = None
            for idx, line in enumerate(fh, 1):
                if n is not None and idx >= n:
                    break
                try:
                    val = int(line.rstrip('\n'))
                except (TypeError, ValueError):
                    raise ValidationError("Line %d is not an integer." % idx)
                if last_val is not None and last_val + 3 == val:
                    raise ValidationError("Line %d is 3 more than line %d"
                                          % (idx, idx-1))
                last_val = val

    # The hook is ``_validate_``, but the public method exposed by the
    # Framework is ``validate``.
    def _validate_(self, level):
        record_map = {'min': 5, 'max': None}
        self._validate_n_ints(record_map[level])

format_instance = IntSequenceFormat(temp_dir.name, mode='r')
format_instance.validate()  # Shouldn't error!

In the fictional format example above, when validate is called with level='min', the _validate_ hook will check the first 5 records, otherwise, when level='max', it will check the entire file.

Astute observers might notice that the method defined in the IntSequenceFormat is called _validate_, but the method called on the format_instance was validate — this is because defining format validation is optional (although highly recommended!). Every format has a validate method available to interfaces (for performing ad-hoc validation), the framework will check for the presence of a _validate_ method on the format in question, and will include that method as part of more general validations that the framework will perform. The aim here is that the framework is capable of ensuring common basic patterns, like presence of required files, while the _validate_ method is the place for the format developer to declare any special “business” logic necessary for ensuring the validity of their format.

Text File Formats

The TextFileFormat is for creating text-based formats (e.g. FASTQ, TSV, etc.). An example of one of these formats is the DNAFASTAFormat, used for storing FASTA data.

Note

This format defines a sniff hook, instead of _validate_ - this is a now-deprecated form of validation that is being replaced with the multi-level validation supported with _validate_.

Binary File Formats

The BinaryFileFormat is for creating binary formats (e.g. BIOM, gzip, etc.). An example of one of these formats is the FastqGzFormat, the format for gzipped FASTQ files.

Directory Formats

While many formats can accurately be described using a single file, many formats exist that require the presence of more than one file present together as a set. QIIME 2 allows more than one FileFormat to be combined together as a DirectoryFormat. The exciting thing about this is that all of the sniffing, validation, and type-safety of the individual file formats is multiplied by however many members are expected to be present within the DirectoryFormat!

Fixed Layouts

Some directory layouts can be accurately described with a fixed number of members. An example of this is the EMPPairedEndDirFmt — this directory format should always be composed of three FastqGzFormat files — one for the forward reads, one for the reverse reads, and one for the barcodes. The FastqGzFormat is defined once (the format doesn’t need to know about the sematic difference between biological reads and barcode reads).

class EMPPairedEndDirFmt(model.DirectoryFormat):
    forward = model.File(r'forward.fastq.gz', format=FastqGzFormat)
    reverse = model.File(r'reverse.fastq.gz', format=FastqGzFormat)
    barcodes = model.File(r'barcodes.fastq.gz', format=FastqGzFormat)

The individual members are defined using the File class.

Variable Layouts

While some layouts are accurately described with a fixed set of members, others are highly variable, preventing formats from accurately knowing how many files to expect in its payload. An example of this kind of format are any of the demultiplexed file formats — when sequences are demultiplexed there is one (or two) files per sample, but how many samples are there? One study might have 5 samples, while another has 5000. For these situations the DirectoryFormat can be configured to watch for set pattern of filenames present in its payload.

class CasavaOneEightSingleLanePerSampleDirFmt(model.DirectoryFormat):
    sequences = model.FileCollection(
        r'.+_.+_L[0-9][0-9][0-9]_R[12]_001\.fastq\.gz',
        format=FastqGzFormat)

    @sequences.set_path_maker
    def sequences_path_maker(self, sample_id, barcode_id, lane_number,
                             read_number):
        return '%s_%s_L%03d_R%d_001.fastq.gz' % (sample_id, barcode_id,
                                                 lane_number, read_number)

Single File Directory Formats

Currently QIIME 2 requires that all formats registered to a Semantic Type be a directory format, which would be a major pain in the case of the single file formats detailed above. For those cases, there exists a factory for quickly constructing directory layouts that contain only a single file. This requirement might be removed in the future, but for now it is a necessary evil (and also isn’t too much extra work for format developers).

DNASequencesDirectoryFormat = model.SingleFileDirectoryFormat(
    'DNASequencesDirectoryFormat', 'dna-sequences.fasta', DNAFASTAFormat)

Associating Formats with a Type

Formats on their own aren’t of much use - it is only once they are registered as a representation of a Semantic Type that things become interesting.

plugin.register_formats(EMPPairedEndDirFmt)
# ``RawSequences`` is a Semantic Type
plugin.register_semantic_types(RawSequences, EMPPairedEndSequences)