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galaxy.tools.util package

Utilities used by various Galaxy tools

FIXME: These are used by tool scripts, not the framework, and should not live

in this package.

Subpackages

• galaxy.tools.util.galaxyops package
  • warn()
  • fail()
  • parse_cols_arg()
  • default_printer()
  • skipped()

Submodules

galaxy.tools.util.maf_utilities module

Provides wrappers and utilities for working with MAF files and alignments.

galaxy.tools.util.maf_utilities.maketrans()

Return a translation table usable for str.translate().

If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.

galaxy.tools.util.maf_utilities.src_split(src)

galaxy.tools.util.maf_utilities.src_merge(spec, chrom, contig=None)

galaxy.tools.util.maf_utilities.get_species_in_block(block)

galaxy.tools.util.maf_utilities.tool_fail(msg='Unknown Error')

class galaxy.tools.util.maf_utilities.TempFileHandler(max_open_files=None, **kwds)

Bases: object

Handles creating, opening, closing, and deleting of Temp files, with a maximum number of files open at one time.

DEFAULT_MAX_OPEN_FILES = 32768.0

__init__(max_open_files=None, **kwds)

get_open_tempfile(index=None, **kwds)

close(index, delete=False)

flush(index)

class galaxy.tools.util.maf_utilities.RegionAlignment(size: int, species=None, temp_file_handler=None)

Bases: object

DNA_COMPLEMENT = {65: 84, 67: 71, 71: 67, 84: 65, 97: 116, 99: 103, 103: 99, 116: 97}

MAX_SEQUENCE_SIZE = 9223372036854775807

__init__(size: int, species=None, temp_file_handler=None)

add_species(species: str)

get_species_names(skip=None)

get_sequence(species: str)

get_sequence_reverse_complement(species: str)

set_position(index, species, base)

set_range(index: int, species: str, bases)

flush(species=None)

class galaxy.tools.util.maf_utilities.GenomicRegionAlignment(start, end, species=None, temp_file_handler=None)

Bases: RegionAlignment

__init__(start, end, species=None, temp_file_handler=None)

sequences: Dict[str, int]

class galaxy.tools.util.maf_utilities.SplicedAlignment(exon_starts, exon_ends, species=None, temp_file_handler=None)

Bases: object

DNA_COMPLEMENT = {65: 84, 67: 71, 71: 67, 84: 65, 97: 116, 99: 103, 103: 99, 116: 97}

__init__(exon_starts, exon_ends, species=None, temp_file_handler=None)

get_species_names(skip=None)

get_sequence(species)

get_sequence_reverse_complement(species)

property start

property end

galaxy.tools.util.maf_utilities.maf_index_by_uid(maf_uid, index_location_file)

galaxy.tools.util.maf_utilities.open_or_build_maf_index(maf_file, index_filename, species=None)

galaxy.tools.util.maf_utilities.build_maf_index_species_chromosomes(filename, index_species=None)

galaxy.tools.util.maf_utilities.build_maf_index(maf_file, species=None)

galaxy.tools.util.maf_utilities.component_overlaps_region(c, region)

galaxy.tools.util.maf_utilities.chop_block_by_region(block, src, region, species=None, mincols=0)

galaxy.tools.util.maf_utilities.orient_block_by_region(block, src, region, force_strand=None)

galaxy.tools.util.maf_utilities.get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None)

galaxy.tools.util.maf_utilities.get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None)

galaxy.tools.util.maf_utilities.iter_blocks_split_by_src(block, src)

galaxy.tools.util.maf_utilities.iter_blocks_split_by_species(block, species=None)

galaxy.tools.util.maf_utilities.get_chopped_blocks_for_region(index, src, region, species=None, mincols=0)

galaxy.tools.util.maf_utilities.get_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0)

galaxy.tools.util.maf_utilities.get_region_alignment(index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None)

galaxy.tools.util.maf_utilities.reduce_block_by_primary_genome(block, species, chromosome, region_start)

galaxy.tools.util.maf_utilities.fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True)

galaxy.tools.util.maf_utilities.get_spliced_region_alignment(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None)

galaxy.tools.util.maf_utilities.line_enumerator(lines, comment_start='#')

galaxy.tools.util.maf_utilities.get_starts_ends_fields_from_gene_bed(line)

galaxy.tools.util.maf_utilities.iter_components_by_src(block, src)

galaxy.tools.util.maf_utilities.get_components_by_src(block, src)

galaxy.tools.util.maf_utilities.iter_components_by_src_start(block, src)

galaxy.tools.util.maf_utilities.get_components_by_src_start(block, src)

galaxy.tools.util.maf_utilities.sort_block_components_by_block(block1, block2)

galaxy.tools.util.maf_utilities.get_species_in_maf(maf_filename)

galaxy.tools.util.maf_utilities.parse_species_option(species)

galaxy.tools.util.maf_utilities.remove_temp_index_file(index_filename)

galaxy.tools.util.maf_utilities.get_fasta_header(component, attributes=None, suffix=None)

galaxy.tools.util.maf_utilities.get_attributes_from_fasta_header(header)

galaxy.tools.util.maf_utilities.iter_fasta_alignment(filename)