dolomite_ranges package

Submodules

dolomite_ranges.read_genomic_ranges module

dolomite_ranges.read_genomic_ranges.read_genomic_ranges(path, metadata, **kwargs)[source]

Load genomic ranges into a GenomicRanges object.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

  • path (str) – Path to the directory containing the object.

  • metadata (Optional[dict]) – Metadata for the object.

  • kwargs – Further arguments, ignored.

Return type:

GenomicRanges

Returns:

A GenomicRanges object.

dolomite_ranges.read_genomic_ranges_list module

dolomite_ranges.read_genomic_ranges_list.read_genomic_ranges_list(path, metadata, **kwargs)[source]

Load genomic ranges into a CompressedGenomicRangesList object.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

  • path (str) – Path to the directory containing the object.

  • metadata (Optional[dict]) – Metadata for the object.

  • kwargs – Further arguments, ignored.

Return type:

CompressedGenomicRangesList

Returns:

A CompressedGenomicRangesList object.

dolomite_ranges.read_sequence_information module

dolomite_ranges.read_sequence_information.read_sequence_information(path, metadata, **kwargs)[source]

Load sequence information into a SeqInfo object.

This method should generally not be called directly but instead be invoked by read_object().

Parameters:

  • path (str) – Path to the directory containing the object.

  • metadata (Optional[dict]) – Metadata for the object.

  • kwargs – Further arguments, ignored.

Return type:

SeqInfo

Returns:

A SeqInfo object.

dolomite_ranges.save_genomic_ranges module

dolomite_ranges.save_genomic_ranges.save_genomic_ranges(x, path, data_frame_args=None, **kwargs)[source]

Method for saving GenomicRanges objects to their corresponding file representations, see save_object() for details.

Parameters:

  • x (GenomicRanges) – Object to be staged.

  • path (str) – Path to a directory in which to save x.

  • data_frame_args (Optional[dict]) – Further arguments to pass to the save_object method for mcols.

  • kwargs – Further arguments to be passed to individual methods.

Returns:

x is saved to path.

dolomite_ranges.save_genomic_ranges_list module

dolomite_ranges.save_genomic_ranges_list.save_compressed_genomic_ranges_list(x, path, data_frame_args=None, **kwargs)[source]

Method for saving CompressedGenomicRangesList objects to their corresponding file representations, see save_object() for details.

Parameters:

  • x (CompressedGenomicRangesList) – Object to be staged.

  • path (str) – Path to a directory in which to save x.

  • data_frame_args (Optional[dict]) – Further arguments to pass to the save_object method for mcols.

  • kwargs – Further arguments to be passed to individual methods.

Returns:

x is saved to path.

dolomite_ranges.save_sequence_information module

dolomite_ranges.save_sequence_information.save_sequence_information(x, path, **kwargs)[source]

Save Sequence information to disk.

Parameters:

  • x (SeqInfo) – Object to be saved.

  • path (str) – Path to a directory in which to save x.

  • kwargs – Further arguments to be passed to individual methods.

Returns:

x is saved to path.

Module contents