Commit ba0108a9 authored by Lucille Delisle's avatar Lucille Delisle
Browse files

format with black

parent 03314ef4

lib/galaxy/datatypes/tabular.py

+9 −41
Original line number Diff line number Diff line
@@ -1803,24 +1803,9 @@ class Tabix(Tabular): 
        optional=True,

    )



    MetadataElement(

        name="chromCol",

        default=1,

        desc="Chrom column",

        param=metadata.ColumnParameter

    )

    MetadataElement(

        name="startCol",

        default=2,

        desc="Start column",

        param=metadata.ColumnParameter

    )

    MetadataElement(

        name="endCol",

        default=3,

        desc="End column",

        param=metadata.ColumnParameter

    )

    MetadataElement(name="chromCol", default=1, desc="Chrom column", param=metadata.ColumnParameter)

    MetadataElement(name="startCol", default=2, desc="Start column", param=metadata.ColumnParameter)

    MetadataElement(name="endCol", default=3, desc="End column", param=metadata.ColumnParameter)



    def sniff(self, filename):

        # Check that the file is compressed with bgzip (not gzip), i.e. the
@@ -1852,13 +1837,14 @@ class Tabix(Tabular): 
                    start_col=dataset.metadata.startCol,

                    end_col=dataset.metadata.endCol,

                    keep_original=True,

                    force=True

                    force=True,

                )

            except Exception as e:

                raise Exception(f"Error setting VCF.gz metadata: {util.unicodify(e)}")

            else:

                dataset.metadata.tabix_index = index_file





class JuicerMediumTabix(Tabix):

    """

    Class describing a tabix file built from a juicer medium format:
@@ -1874,27 +1860,9 @@ class JuicerMediumTabix(Tabix): 


    file_ext = "juicer.medium.tabix"



    MetadataElement(

        name="chromCol",

        default=3,

        desc="Chrom column",

        param=metadata.ColumnParameter

    )

    MetadataElement(

        name="startCol",

        default=4,

        desc="Start column",

        param=metadata.ColumnParameter

    )

    MetadataElement(

        name="endCol",

        default=4,

        desc="End column",

        param=metadata.ColumnParameter

    )

    MetadataElement(name="chromCol", default=3, desc="Chrom column", param=metadata.ColumnParameter)

    MetadataElement(name="startCol", default=4, desc="Start column", param=metadata.ColumnParameter)

    MetadataElement(name="endCol", default=4, desc="End column", param=metadata.ColumnParameter)



    def set_meta(self, dataset, metadata_tmp_files_dir=None, **kwd):

        super().set_meta(dataset,

                         metadata_tmp_files_dir=metadata_tmp_files_dir,

                         build_index=True,

                         **kwd)
 
        super().set_meta(dataset, metadata_tmp_files_dir=metadata_tmp_files_dir, build_index=True, **kwd)