Commit 8ce7bd8f authored by Lucille Delisle's avatar Lucille Delisle
Browse files

create a new class IntervalTabix

parent 08bb9722

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

+5 −5
Original line number Diff line number Diff line
@@ -475,8 +475,11 @@ 
    <datatype extension="protobuf2" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data." display_in_upload="true"/>

    <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.tabular:Tabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="juicer.medium.tabix" type="galaxy.datatypes.tabular:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>

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

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

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

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

    <datatype extension="gff_tabix" 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"/>
@@ -1197,8 +1200,5 @@ 
    <sniffer type="galaxy.datatypes.binary:OxliSubset"/>

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

    <sniffer type="galaxy.datatypes.neo4j:Neo4jDBzip"/>

    <sniffer type="galaxy.datatypes.tabular:VcfGz"/>

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

    <sniffer type="galaxy.datatypes.tabular:Tabix"/>

  </sniffers>

</datatypes>

lib/galaxy/datatypes/interval.py

+109 −0
Original line number Diff line number Diff line
@@ -7,6 +7,8 @@ import sys 
import tempfile

from urllib.parse import quote_plus



import pysam



from bx.intervals.io import (

    GenomicIntervalReader,

    ParseError,
@@ -1729,6 +1731,113 @@ class ScIdx(Tabular): 
        return False





class IntervalTabix(Interval):

    """

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

    As tabix is just a bgzip with an index

    """



    file_ext = "tabix"

    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 define sniff as the index would be created before the metadata on columns set.

    # def sniff(self, filename):

    #     # Check that the file is compressed with bgzip (not gzip), i.e. the

    #     # compressed format is BGZF, as explained in

    #     # http://samtools.github.io/hts-specs/SAMv1.pdf

    #     with open(filename, "rb") as fh:

    #         fh.seek(-28, 2)

    #         last28 = fh.read()

    #         return binascii.hexlify(last28) == b"1f8b08040000000000ff0600424302001b0003000000000000000000"



    # 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"



    # 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"





class GffTabix(IntervalTabix):

    """

    Class describing a tabix file built from a bed file

    """



    file_ext = "gff.tabix"



    # 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

lib/galaxy/datatypes/tabular.py

+0 −87
Original line number Diff line number Diff line
@@ -1779,90 +1779,3 @@ class CMAP(TabularData): 
            dataset.metadata.column_types = cleaned_column_types

            dataset.metadata.columns = number_of_columns

            dataset.metadata.delimiter = "\t"
 




class Tabix(Tabular):

    """

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

    As tabix is just a bgzip with an index

    """



    file_ext = "tabix"

    edam_format = "format_3616"

    compressed = True

    compressed_format = "gzip"



    # Add metadata elements

    MetadataElement(

        name="tabix_index",

        desc="Tabix Index File",

        param=metadata.FileParameter,

        file_ext="tbi",

        readonly=True,

        visible=False,

        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)



    def sniff(self, filename):

        # Check that the file is compressed with bgzip (not gzip), i.e. the

        # compressed format is BGZF, as explained in

        # http://samtools.github.io/hts-specs/SAMv1.pdf

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

            fh.seek(-28, 2)

            last28 = fh.read()

            return binascii.hexlify(last28) == b"1f8b08040000000000ff0600424302001b0003000000000000000000"



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

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

        super().set_meta(dataset, **kwd)

        if build_index:

            # 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(Tabix):

    """

    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"



    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)

lib/galaxy/datatypes/test/test.tabix

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