Unverified Commit 0d0e2a1a authored by Martin Cech's avatar Martin Cech Committed by GitHub
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Merge pull request #18507 from TomHarrop/datatype_pod5_backport 

[24.1] Backport pod5 datatype
parents 21e7a222 011a5914

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

+2 −0
Original line number Diff line number Diff line
@@ -361,6 +361,7 @@ 
    <datatype extension="fast5.tar.gz" type="galaxy.datatypes.binary:Fast5ArchiveGz" display_in_upload="true"/>

    <datatype extension="fast5.tar.bz2" type="galaxy.datatypes.binary:Fast5ArchiveBz2" display_in_upload="true"/>

    <datatype extension="fast5.tar.xz" type="galaxy.datatypes.binary:Fast5ArchiveXz" display_in_upload="true"/>

    <datatype extension="pod5" type="galaxy.datatypes.binary:Pod5" display_in_upload="true"/>

    <datatype extension="peptideshaker_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>

    <datatype extension="percin" type="galaxy.datatypes.tabular:Tabular" subclass="true"/>

    <datatype extension="percout" type="galaxy.datatypes.xml:GenericXml" subclass="true"/>
@@ -1079,6 +1080,7 @@ 
    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveXz"/>

    <sniffer type="galaxy.datatypes.binary:Fast5ArchiveBz2"/>

    <sniffer type="galaxy.datatypes.binary:Fast5Archive"/>

    <sniffer type="galaxy.datatypes.binary:Pod5"/>

    <sniffer type="galaxy.datatypes.binary:Meryldb" />

    <sniffer type="galaxy.datatypes.binary:Bref3" />

    <sniffer type="galaxy.datatypes.binary:PostgresqlArchive"/>

lib/galaxy/datatypes/binary.py

+25 −0
Original line number Diff line number Diff line
@@ -3759,6 +3759,31 @@ class Fast5ArchiveBz2(Fast5Archive): 
        return Fast5Archive.sniff(self, filename)





class Pod5(Binary):

    """

    Class describing a POD5 file. The POD5 Format Specification is at

    https://pod5-file-format.readthedocs.io/en/latest/SPECIFICATION.html



    >>> from galaxy.datatypes.sniff import get_test_fname

    >>> fname = get_test_fname('test.pod5')

    >>> Pod5().sniff(fname)

    True

    >>> fname = get_test_fname('test.fast5.tar')

    >>> Pod5().sniff(fname)

    False

    """



    file_ext = "pod5"



    def sniff(self, filename: str) -> bool:

        expected_signature = bytes([0x8B, 0x50, 0x4F, 0x44, 0x0D, 0x0A, 0x1A, 0x0A])

        with open(filename, "rb") as f:

            first_8_bytes = f.read(8)

            f.seek(-8, 2)

            last_8_bytes = f.read(8)

            return first_8_bytes == expected_signature and last_8_bytes == expected_signature





class SearchGuiArchive(CompressedArchive):

    """Class describing a SearchGUI archive"""

lib/galaxy/datatypes/test/test.pod5

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