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
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.
- 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 = 32768.0
- class galaxy.tools.util.maf_utilities.RegionAlignment(size, species=None, temp_file_handler=None)[source]
Bases:
object
- DNA_COMPLEMENT = {65: 84, 67: 71, 71: 67, 84: 65, 97: 116, 99: 103, 103: 99, 116: 97}
- MAX_SEQUENCE_SIZE = 9223372036854775807
- class galaxy.tools.util.maf_utilities.GenomicRegionAlignment(start, end, species=None, temp_file_handler=None)[source]
Bases:
RegionAlignment
- class galaxy.tools.util.maf_utilities.SplicedAlignment(exon_starts, exon_ends, species=None, temp_file_handler=None)[source]
Bases:
object
- DNA_COMPLEMENT = {65: 84, 67: 71, 71: 67, 84: 65, 97: 116, 99: 103, 103: 99, 116: 97}
- property start
- property end
- 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.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.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]