Merge pull request #20874 from abretaud/hic_datatype (59b5b6be) · Commits · NDIP / Galaxy

lib/galaxy/config/sample/datatypes_conf.xml.sample

+3 −1

Original line number	Diff line number	Diff line
		@@ -239,6 +239,7 @@
		<datatype extension="mbi" type="galaxy.datatypes.binary:H5" subclass="true" mimetype="application/octet-stream" display_in_upload="true" description="MBI is MOBILion's proprietary HDF5-based format for its ion mobility mass spectrometry data." />
		<datatype extension="hyphy_results.json" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
		<datatype extension="hivtrace" type="galaxy.datatypes.text:Json" mimetype="application/json" subclass="true" display_in_upload="false"/>
		<datatype extension="hic" type="galaxy.datatypes.binary:Hic" mimetype="application/octet-stream" display_in_upload="true"/>
		<datatype extension="cool" type="galaxy.datatypes.binary:Cool" mimetype="application/octet-stream" display_in_upload="true"/>
		<datatype extension="mcool" type="galaxy.datatypes.binary:MCool" mimetype="application/octet-stream" display_in_upload="true"/>
		<datatype extension="h5mlm" type="galaxy.datatypes.binary:H5MLM" mimetype="application/octet-stream" display_in_upload="true"/>
		@@ -1223,6 +1224,7 @@
		<sniffer type="galaxy.datatypes.binary:NcbiTaxonomySQlite"/>
		<sniffer type="galaxy.datatypes.binary:SQlite"/>
		<sniffer type="galaxy.datatypes.binary:H5MLM"/>
		<sniffer type="galaxy.datatypes.binary:Hic"/>
		<sniffer type="galaxy.datatypes.binary:Cool"/>
		<sniffer type="galaxy.datatypes.binary:MCool"/>
		<sniffer type="galaxy.datatypes.binary:Loom"/>

lib/galaxy/datatypes/binary.py

+60 −0

Original line number	Diff line number	Diff line
		@@ -4770,3 +4770,63 @@ class Numpy(Binary):
		return dataset.peek
		except Exception:
		return f"Binary numpy file ({nice_size(dataset.get_size())})"


		@build_sniff_from_prefix
		class Hic(Binary):
		"""
		Hic: highly compressed binary file that stores contact matrices
		from multiple resolutions in a clever way, allowing random access.
		https://github.com/aidenlab/hic-format

		>>> from galaxy.datatypes.sniff import get_test_fname
		>>> fname = get_test_fname('merlin.hic')
		>>> Hic().sniff(fname)
		True
		>>> fname = get_test_fname('test.mz5')
		>>> Hic().sniff(fname)
		False
		"""

		file_ext = "hic"

		MetadataElement(
		name="version",
		default="",
		param=MetadataParameter,
		desc="Version of the HiC file format",
		readonly=True,
		visible=True,
		no_value=0,
		optional=True,
		)

		def __init__(self, **kwd):
		super().__init__(**kwd)
		self._magic = b"HIC"

		def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
		return file_prefix.startswith_bytes(self._magic)

		def set_peek(self, dataset: DatasetProtocol, **kwd) -> None:
		if not dataset.dataset.purged:
		dataset.peek = "Binary HiC file"
		dataset.blurb = f"{nice_size(dataset.get_size())}"
		dataset.blurb += f"\nHiC Format v{dataset.metadata.version}"
		else:
		dataset.peek = "file does not exist"
		dataset.blurb = "file purged from disk"

		def display_peek(self, dataset: DatasetProtocol) -> str:
		try:
		return dataset.peek
		except Exception:
		return f"Binary HiC file ({nice_size(dataset.get_size())})"

		def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd) -> None:
		"""
		Set metadata for HiC file.
		"""
		with open(dataset.get_file_name(), "rb") as handle:
		header_bytes = handle.read(8)
		dataset.metadata.version = struct.unpack("<i", header_bytes[4:8])[0]

lib/galaxy/datatypes/test/merlin.hic

0 → 100644

+931 B

File added.

No diff preview for this file type.

View file