util Package¶
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.
maf_utilities
Module¶
Provides wrappers and utilities for working with MAF files and alignments.
-
class
galaxy.tools.util.maf_utilities.
GenomicRegionAlignment
(start, end, species=[], temp_file_handler=None)[source]¶
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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 !"#$%&\'()*+,-./0123456789:;<=>?@TBGDEFCHIJKLMNOPQRSAUVWXYZ[\\]^_`tbgdefchijklmnopqrsauvwxyz{|}~\x7f\x80\x81\x82\x83\x84\x85\x86\x87\x88\x89\x8a\x8b\x8c\x8d\x8e\x8f\x90\x91\x92\x93\x94\x95\x96\x97\x98\x99\x9a\x9b\x9c\x9d\x9e\x9f\xa0\xa1\xa2\xa3\xa4\xa5\xa6\xa7\xa8\xa9\xaa\xab\xac\xad\xae\xaf\xb0\xb1\xb2\xb3\xb4\xb5\xb6\xb7\xb8\xb9\xba\xbb\xbc\xbd\xbe\xbf\xc0\xc1\xc2\xc3\xc4\xc5\xc6\xc7\xc8\xc9\xca\xcb\xcc\xcd\xce\xcf\xd0\xd1\xd2\xd3\xd4\xd5\xd6\xd7\xd8\xd9\xda\xdb\xdc\xdd\xde\xdf\xe0\xe1\xe2\xe3\xe4\xe5\xe6\xe7\xe8\xe9\xea\xeb\xec\xed\xee\xef\xf0\xf1\xf2\xf3\xf4\xf5\xf6\xf7\xf8\xf9\xfa\xfb\xfc\xfd\xfe\xff'¶
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MAX_SEQUENCE_SIZE
= 9223372036854775807¶
-
-
class
galaxy.tools.util.maf_utilities.
SplicedAlignment
(exon_starts, exon_ends, species=[], temp_file_handler=None)[source]¶ Bases:
object
-
DNA_COMPLEMENT
= '\x00\x01\x02\x03\x04\x05\x06\x07\x08\t\n\x0b\x0c\r\x0e\x0f\x10\x11\x12\x13\x14\x15\x16\x17\x18\x19\x1a\x1b\x1c\x1d\x1e\x1f !"#$%&\'()*+,-./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'¶
-
end
¶
-
start
¶
-
-
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
= 512¶
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-
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]¶
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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]¶
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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]¶
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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_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.
get_spliced_region_alignment
(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None)[source]¶
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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.
orient_block_by_region
(block, src, region, force_strand=None)[source]¶