Merge pull request #15024 from lldelisle/tabix_download_22.05

    <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data." display_in_upload="true"/>

    <datatype extension="onnx" type="galaxy.datatypes.binary:Binary" subclass="true" description="ONNX (Open neural network exchange) is data format for storing and sharing machine learning and deep learning models." display_in_upload="true"/>

    <datatype extension="tabix" type="galaxy.datatypes.binary:Binary" subclass="true"/>

    <datatype extension="interval_tabix.gz" type="galaxy.datatypes.interval:IntervalTabix" mimetype="application/octet-stream" />

    <datatype extension="juicer_medium_tabix.gz" type="galaxy.datatypes.interval:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>

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

    <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

      <display file="igv/vcf.xml"/>

import tempfile

from urllib.parse import quote_plus

import pysam

from bx.intervals.io import (

    GenomicIntervalReader,

    ParseError,

        return False

class IntervalTabix(Interval):

    """

    Class describing the bgzip format (http://samtools.github.io/hts-specs/SAMv1.pdf)

    As tabix is just a bgzip sorted for chr,start,end with an index

    """

    file_ext = "interval_tabix.gz"

    edam_format = "format_3616"

    compressed = True

    compressed_format = "gzip"

    # The MetadataElements are readonly so the user cannot change them (as the index is generated only once)

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

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

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

    # Add metadata elements

    MetadataElement(

        name="tabix_index",

        desc="Tabix Index File",

        param=metadata.FileParameter,

        file_ext="tbi",

        readonly=True,

        visible=False,

        optional=True,

    )

    # We don't want to have a good sniff as the index would be created before the metadata on columns is set.

    def sniff_prefix(self, file_prefix: FilePrefix):

        return False

    # Ideally the tabix_index would be regenerated when the metadataElements are updated

    def set_meta(self, dataset, overwrite=True, first_line_is_header=False, metadata_tmp_files_dir=None, **kwd):

        # We don't use the method Interval.set_meta as we don't want to guess the columns for chr start end

        Tabular.set_meta(self, dataset, overwrite=overwrite, skip=0)

        # Try to create the index for the Tabix file.

        # These metadata values are not accessible by users, always overwrite

        index_file = dataset.metadata.tabix_index

        if not index_file:

            index_file = dataset.metadata.spec["tabix_index"].param.new_file(

                dataset=dataset, metadata_tmp_files_dir=metadata_tmp_files_dir

            )

        try:

            # tabix_index columns are 0-based while in the command line it is 1-based

            pysam.tabix_index(

                dataset.file_name,

                index=index_file.file_name,

                seq_col=dataset.metadata.chromCol - 1,

                start_col=dataset.metadata.startCol - 1,

                end_col=dataset.metadata.endCol - 1,

                keep_original=True,

                force=True,

            )

        except Exception as e:

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

        else:

            dataset.metadata.tabix_index = index_file

class JuicerMediumTabix(IntervalTabix):

    """

    Class describing a tabix file built from a juicer medium format:

    https://github.com/aidenlab/juicer/wiki/Pre#medium-format

    <readname> <str1> <chr1> <pos1> <frag1> <str2> <chr2> <pos2> <frag2> <mapq1> <mapq2>

    str = strand (0 for forward, anything else for reverse)

    chr = chromosome (must be a chromosome in the genome)

    pos = position

    frag = restriction site fragment

    mapq = mapping quality score

    """

    file_ext = "juicer_medium_tabix.gz"

    # The MetadataElements are readonly so the user cannot change them (as the index is generated only once)

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

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

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

class BedTabix(IntervalTabix):

    """

    Class describing a tabix file built from a bed file

    """

    file_ext = "bed_tabix.gz"

class GffTabix(IntervalTabix):

    """

    Class describing a tabix file built from a bed file

    """

    file_ext = "gff_tabix.gz"

    # The MetadataElements are readonly so the user cannot change them (as the index is generated only once)

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

    MetadataElement(name="endCol", default=5, desc="End column", param=metadata.ColumnParameter, readonly=True)

if __name__ == "__main__":

    import doctest