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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¶
Submodules¶
galaxy.tools.util.maf_utilities module¶
Provides wrappers and utilities for working with MAF files and alignments.
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galaxy.tools.util.maf_utilities.
maketrans
(x, y=None, z=None, /)¶ 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
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DNA_COMPLEMENT
= {65: 84, 67: 71, 71: 67, 84: 65, 97: 116, 99: 103, 103: 99, 116: 97}¶
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MAX_SEQUENCE_SIZE
= 9223372036854775807¶
-
-
class
galaxy.tools.util.maf_utilities.
GenomicRegionAlignment
(start, end, species=None, temp_file_handler=None)[source]¶
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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}¶
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__init__
(exon_starts, exon_ends, species=None, temp_file_handler=None)[source]¶ Initialize self. See help(type(self)) for accurate signature.
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property
start
¶
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property
end
¶
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galaxy.tools.util.maf_utilities.
open_or_build_maf_index
(maf_file, index_filename, species=None)[source]¶
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galaxy.tools.util.maf_utilities.
build_maf_index_species_chromosomes
(filename, index_species=None)[source]¶
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galaxy.tools.util.maf_utilities.
chop_block_by_region
(block, src, region, species=None, mincols=0)[source]¶
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galaxy.tools.util.maf_utilities.
orient_block_by_region
(block, src, region, force_strand=None)[source]¶
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galaxy.tools.util.maf_utilities.
get_oriented_chopped_blocks_for_region
(index, src, region, species=None, mincols=0, force_strand=None)[source]¶
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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]¶
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galaxy.tools.util.maf_utilities.
get_chopped_blocks_for_region
(index, src, region, species=None, mincols=0)[source]¶
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galaxy.tools.util.maf_utilities.
get_chopped_blocks_with_index_offset_for_region
(index, src, region, species=None, mincols=0)[source]¶
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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]¶
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galaxy.tools.util.maf_utilities.
reduce_block_by_primary_genome
(block, species, chromosome, region_start)[source]¶
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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]¶