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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.

Submodules

galaxy.tools.util.maf_utilities module

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

galaxy.tools.util.maf_utilities.src_split(src)[source]
galaxy.tools.util.maf_utilities.src_merge(spec, chrom, contig=None)[source]
galaxy.tools.util.maf_utilities.get_species_in_block(block)[source]
galaxy.tools.util.maf_utilities.tool_fail(msg='Unknown Error')[source]
class galaxy.tools.util.maf_utilities.TempFileHandler(max_open_files=None, **kwds)[source]

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 = 524288
__init__(max_open_files=None, **kwds)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_open_tempfile(index=None, **kwds)[source]
close(index, delete=False)[source]
flush(index)[source]
class galaxy.tools.util.maf_utilities.RegionAlignment(size, species=[], temp_file_handler=None)[source]

Bases: object

DNA_COMPLEMENT = '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\x1d\x1e\x1f !"#$%&\'()*+,-./0123456789:;<=>?@TBGDEFCHIJKLMNOPQRSAUVWXYZ[\\]^_`tbgdefchijklmnopqrsauvwxyz{|}~\x7f\x80\x81\x82\x83\x84\x85\x86\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xcc\xcd\xce\xcf\xd0\xd1\xd2\xd3\xd4\xd5\xd6\xd7\xd8\xd9\xda\xdb\xdc\xdd\xde\xdf\xe0\xe1\xe2\xe3\xe4\xe5\xe6\xe7\xe8\xe9\xea\xeb\xec\xed\xee\xef\xf0\xf1\xf2\xf3\xf4\xf5\xf6\xf7\xf8\xf9\xfa\xfb\xfc\xfd\xfe\xff'
MAX_SEQUENCE_SIZE = 9223372036854775807
__init__(size, species=[], temp_file_handler=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

add_species(species)[source]
get_species_names(skip=[])[source]
get_sequence(species)[source]
get_sequence_reverse_complement(species)[source]
set_position(index, species, base)[source]
set_range(index, species, bases)[source]
flush(species=None)[source]
class galaxy.tools.util.maf_utilities.GenomicRegionAlignment(start, end, species=[], temp_file_handler=None)[source]

Bases: galaxy.tools.util.maf_utilities.RegionAlignment

__init__(start, end, species=[], temp_file_handler=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

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

Bases: object

DNA_COMPLEMENT = '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\x1d\x1e\x1f !"#$%&\'()*+,-./0123456789:;<=>?@TBGDEFCHIJKLMNOPQRSAUVWXYZ[\\]^_`tbgdefchijklmnopqrsauvwxyz{|}~\x7f\x80\x81\x82\x83\x84\x85\x86\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xcc\xcd\xce\xcf\xd0\xd1\xd2\xd3\xd4\xd5\xd6\xd7\xd8\xd9\xda\xdb\xdc\xdd\xde\xdf\xe0\xe1\xe2\xe3\xe4\xe5\xe6\xe7\xe8\xe9\xea\xeb\xec\xed\xee\xef\xf0\xf1\xf2\xf3\xf4\xf5\xf6\xf7\xf8\xf9\xfa\xfb\xfc\xfd\xfe\xff'
__init__(exon_starts, exon_ends, species=[], temp_file_handler=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

get_species_names(skip=[])[source]
get_sequence(species)[source]
get_sequence_reverse_complement(species)[source]
start
end
galaxy.tools.util.maf_utilities.maf_index_by_uid(maf_uid, index_location_file)[source]
galaxy.tools.util.maf_utilities.open_or_build_maf_index(maf_file, index_filename, species=None)[source]
galaxy.tools.util.maf_utilities.build_maf_index_species_chromosomes(filename, index_species=None)[source]
galaxy.tools.util.maf_utilities.build_maf_index(maf_file, species=None)[source]
galaxy.tools.util.maf_utilities.component_overlaps_region(c, region)[source]
galaxy.tools.util.maf_utilities.chop_block_by_region(block, src, region, species=None, mincols=0)[source]
galaxy.tools.util.maf_utilities.orient_block_by_region(block, src, region, force_strand=None)[source]
galaxy.tools.util.maf_utilities.get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None)[source]
galaxy.tools.util.maf_utilities.get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None)[source]
galaxy.tools.util.maf_utilities.iter_blocks_split_by_src(block, src)[source]
galaxy.tools.util.maf_utilities.iter_blocks_split_by_species(block, species=None)[source]
galaxy.tools.util.maf_utilities.get_chopped_blocks_for_region(index, src, region, species=None, mincols=0)[source]
galaxy.tools.util.maf_utilities.get_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0)[source]
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)[source]
galaxy.tools.util.maf_utilities.reduce_block_by_primary_genome(block, species, chromosome, region_start)[source]
galaxy.tools.util.maf_utilities.fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True)[source]
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)[source]
galaxy.tools.util.maf_utilities.line_enumerator(lines, comment_start='#')[source]
galaxy.tools.util.maf_utilities.get_starts_ends_fields_from_gene_bed(line)[source]
galaxy.tools.util.maf_utilities.iter_components_by_src(block, src)[source]
galaxy.tools.util.maf_utilities.get_components_by_src(block, src)[source]
galaxy.tools.util.maf_utilities.iter_components_by_src_start(block, src)[source]
galaxy.tools.util.maf_utilities.get_components_by_src_start(block, src)[source]
galaxy.tools.util.maf_utilities.sort_block_components_by_block(block1, block2)[source]
galaxy.tools.util.maf_utilities.get_species_in_maf(maf_filename)[source]
galaxy.tools.util.maf_utilities.parse_species_option(species)[source]
galaxy.tools.util.maf_utilities.remove_temp_index_file(index_filename)[source]
galaxy.tools.util.maf_utilities.get_fasta_header(component, attributes={}, suffix=None)[source]
galaxy.tools.util.maf_utilities.get_attributes_from_fasta_header(header)[source]
galaxy.tools.util.maf_utilities.iter_fasta_alignment(filename)[source]