plastid
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Index
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
Symbols
0-indexed
0-indexed coordinates
1-indexed
1-indexed coordinates
A
add_filter() (plastid.genomics.genome_array.BAMGenomeArray method)
add_from_bigwig() (plastid.genomics.genome_array.BigWigGenomeArray method)
add_from_bowtie() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
add_from_wiggle() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
add_listener() (plastid.util.io.filters.TeeReader method)
add_listeners() (plastid.util.io.filters.TeeReader method)
add_masks() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
add_segments() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
add_three_for_stop_codon() (in module plastid.genomics.roitools)
add_type() (plastid.readers.autosql.AutoSqlDeclaration method)
(plastid.readers.autosql.AutoSqlField method)
(plastid.readers.autosql.SizedAutoSqlField method)
(plastid.readers.autosql.ValuesAutoSqlField method)
alert() (plastid.util.io.filters.TeeListener method)
(plastid.util.io.filters.TestTeeListener method)
alignment
AlignmentParser (class in plastid.util.scriptlib.argparsers)
annotation
AnnotationParser (class in plastid.util.scriptlib.argparsers)
antisense_overlaps() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
append() (plastid.util.unique_fifo.UniqueFIFO method)
apply_operation() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
args (plastid.util.services.exceptions.ArgumentWarning attribute)
(plastid.util.services.exceptions.DataWarning attribute)
(plastid.util.services.exceptions.FileFormatWarning attribute)
(plastid.util.services.exceptions.MalformedFileError attribute)
args_to_comment() (in module plastid.util.io.openers)
argsopener() (in module plastid.util.io.openers)
ArgumentWarning
as_bed() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
as_gff3() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
as_gtf() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
as_igv_str() (plastid.genomics.roitools.GenomicSegment method)
as_psl() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
AssembledFeatureReader (class in plastid.readers.common)
attr (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
AutoSqlDeclaration (class in plastid.readers.autosql)
AutoSqlField (class in plastid.readers.autosql)
B
BackwardReader (class in plastid.util.io.filters)
BAMGenomeArray (class in plastid.genomics.genome_array)
BaseParser (class in plastid.util.scriptlib.argparsers)
BED X+Y
bed_fields (plastid.readers.bigbed.BigBedReader attribute)
BED_Reader (class in plastid.readers.bed)
bed_x_formats (in module plastid.readers.bed)
BigBedGenomeHash (class in plastid.genomics.genome_hash)
BigBedIterator() (in module plastid.readers.bigbed)
BigBedReader (class in plastid.readers.bigbed)
BigWigGenomeArray (class in plastid.genomics.genome_array)
BigWigIterator() (in module plastid.readers.bigwig)
BigWigReader (class in plastid.readers.bigwig)
BinaryParserFactory (class in plastid.util.io.binary)
BowtieReader (class in plastid.readers.bowtie)
BundledPSL_Reader (class in plastid.readers.psl)
C
c_strand (plastid.genomics.roitools.GenomicSegment attribute)
(plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
calcsize() (plastid.util.io.binary.BinaryParserFactory method)
catch_stderr() (in module plastid.util.services.decorators)
catch_stdout() (in module plastid.util.services.decorators)
catch_warnings() (in module plastid.util.services.decorators)
cds_end (plastid.genomics.roitools.Transcript attribute)
cds_genome_end (plastid.genomics.roitools.Transcript attribute)
cds_genome_start (plastid.genomics.roitools.Transcript attribute)
cds_start (plastid.genomics.roitools.Transcript attribute)
center_map() (in module plastid.genomics.genome_array)
CenterMapFactory (class in plastid.genomics.map_factories)
chrom (plastid.genomics.roitools.GenomicSegment attribute)
(plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
chrom_sizes (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
chrom_worker() (in module plastid.bin.crossmap)
chromids (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
chroms (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
chroms() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
clean_invalid() (in module plastid.plotting.plotutils)
close() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
closed (plastid.bin.crossmap.FastaNameReader attribute)
(plastid.readers.bed.BED_Reader attribute)
(plastid.readers.bowtie.BowtieReader attribute)
(plastid.readers.common.AssembledFeatureReader attribute)
(plastid.readers.gff.GFF3_Reader attribute)
(plastid.readers.gff.GFF3_TranscriptAssembler attribute)
(plastid.readers.gff.GTF2_Reader attribute)
(plastid.readers.gff.GTF2_TranscriptAssembler attribute)
(plastid.readers.psl.BundledPSL_Reader attribute)
(plastid.readers.psl.PSL_Reader attribute)
(plastid.util.io.filters.BackwardReader attribute)
(plastid.util.io.filters.ColorWriter attribute)
(plastid.util.io.filters.CommentReader attribute)
(plastid.util.io.filters.CommentWriter attribute)
(plastid.util.io.filters.FunctionReader attribute)
(plastid.util.io.filters.NameDateWriter attribute)
(plastid.util.io.filters.SkipBlankReader attribute)
(plastid.util.io.filters.TeeReader attribute)
(plastid.util.io.openers.NullWriter attribute)
color() (plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.NameDateWriter method)
colored() (in module plastid.util.io.filters)
ColorWriter (class in plastid.util.io.filters)
CommentReader (class in plastid.util.io.filters)
CommentWriter (class in plastid.util.io.filters)
contains() (plastid.genomics.roitools.GenomicSegment method)
count file
counts
covered_by_repetitive() (in module plastid.bin.slidejuncs)
covers() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
crossmap
D
darken() (in module plastid.plotting.colors)
DataWarning
deep sequencing
deprecated() (in module plastid.util.services.decorators)
DMS-seq
do_chart() (in module plastid.bin.cs)
(in module plastid.bin.metagene)
do_count() (in module plastid.bin.cs)
(in module plastid.bin.metagene)
(in module plastid.bin.psite)
do_generate() (in module plastid.bin.cs)
do_scatter() (in module plastid.bin.cs)
dtmp (plastid.readers.gff.GTF2_TranscriptAssembler attribute)
E
end (plastid.genomics.roitools.GenomicSegment attribute)
end-inclusive
equal_enough() (in module plastid.bin.test_table_equality)
escape() (in module plastid.readers.gff_tokens)
escape_GFF3() (in module plastid.readers.gff_tokens)
escape_GTF2() (in module plastid.readers.gff_tokens)
Extended BED
extension_fields (plastid.readers.bigbed.BigBedReader attribute)
F
fa_to_bed() (in module plastid.bin.crossmap)
factory function
false discovery rate
FastaNameReader (class in plastid.bin.crossmap)
FDR
feature
FileFormatWarning
filename (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
fileno() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
filter() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
filterwarnings() (in module plastid.util.services.exceptions)
find_canonicals_in_range() (in module plastid.bin.slidejuncs)
find_known_in_range() (in module plastid.bin.slidejuncs)
find_match_range() (in module plastid.bin.slidejuncs)
find_null_bytes() (in module plastid.util.io.binary)
five_prime_map() (in module plastid.genomics.genome_array)
FivePrimeMapFactory (class in plastid.genomics.map_factories)
fix_name() (in module plastid.bin.reformat_transcripts)
flatten_nested_lists_to_generator() (in module plastid.util.services.lists)
flatten_nested_lists_to_list() (in module plastid.util.services.lists)
flush() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
footprint
format_module_docstring() (in module plastid.util.scriptlib.help_formatters)
formatwarning() (in module plastid.util.services.exceptions)
from_bed() (plastid.genomics.roitools.SegmentChain static method)
(plastid.genomics.roitools.Transcript static method)
from_file() (plastid.genomics.map_factories.StratifiedVariableFivePrimeMapFactory method)
(plastid.genomics.map_factories.VariableFivePrimeMapFactory method)
from_igv_str() (plastid.genomics.roitools.GenomicSegment static method)
from_psl() (plastid.genomics.roitools.SegmentChain static method)
(plastid.genomics.roitools.Transcript static method)
from_str() (plastid.genomics.roitools.GenomicSegment static method)
(plastid.genomics.roitools.SegmentChain static method)
(plastid.genomics.roitools.Transcript static method)
fully-closed
FunctionReader (class in plastid.util.io.filters)
G
genome assembly
genome browser
genome build
GenomeArray (class in plastid.genomics.genome_array)
GenomeHash (class in plastid.genomics.genome_hash)
GenomicSegment (class in plastid.genomics.roitools)
get() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
(plastid.readers.bigbed.BigBedReader method)
(plastid.readers.bigwig.BigWigReader method)
get_alignment_file_parser() (in module plastid.util.scriptlib.argparsers)
get_annotation_file_parser() (in module plastid.util.scriptlib.argparsers)
get_antisense() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_base_ops_from_args() (plastid.util.scriptlib.argparsers.BaseParser method)
get_cds() (plastid.genomics.roitools.Transcript method)
get_chromosome_counts() (plastid.readers.bigwig.BigWigReader method)
get_color_cycle() (in module plastid.plotting.plots)
get_colors_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.PlottingParser method)
get_comments() (plastid.util.io.filters.CommentReader method)
get_counts() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_fasta() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_fig_axes() (in module plastid.plotting.plotutils)
get_figure_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.PlottingParser method)
get_func_code() (in module plastid.util.services.mini2to3)
get_gene() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_genome_array_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.AlignmentParser method)
get_genome_hash_from_args() (plastid.util.scriptlib.argparsers.AnnotationParser method)
(plastid.util.scriptlib.argparsers.MaskParser method)
(plastid.util.scriptlib.argparsers.SequenceParser method)
get_genome_hash_from_mask_args() (in module plastid.util.scriptlib.argparsers)
get_genomic_coordinate() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_identical_attributes() (in module plastid.readers.common)
get_junction_tuple() (in module plastid.genomics.splicing)
get_junctions() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_kde() (in module plastid.plotting.plotutils)
get_mapping() (plastid.genomics.genome_array.BAMGenomeArray method)
get_mask_file_parser() (in module plastid.util.scriptlib.argparsers)
get_masked_counts() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_masked_position_set() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_masks() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_masks_as_segmentchain() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_name() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_nearby_feature_names() (plastid.genomics.genome_hash.GenomeHash method)
get_nearby_features() (plastid.genomics.genome_hash.GenomeHash method)
get_overlapping_features() (plastid.genomics.genome_hash.BigBedGenomeHash method)
(plastid.genomics.genome_hash.GenomeHash method)
(plastid.genomics.genome_hash.TabixGenomeHash method)
get_parser() (plastid.util.scriptlib.argparsers.AlignmentParser method)
(plastid.util.scriptlib.argparsers.AnnotationParser method)
(plastid.util.scriptlib.argparsers.BaseParser method)
(plastid.util.scriptlib.argparsers.MaskParser method)
(plastid.util.scriptlib.argparsers.Parser method)
(plastid.util.scriptlib.argparsers.PlottingParser method)
(plastid.util.scriptlib.argparsers.SequenceParser method)
get_plotting_parser() (in module plastid.util.scriptlib.argparsers)
get_position_list() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_position_set() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_random_sets() (in module plastid.util.services.sets)
get_reads() (plastid.genomics.genome_array.BAMGenomeArray method)
get_reads_and_counts() (plastid.genomics.genome_array.BAMGenomeArray method)
get_rgb255() (in module plastid.plotting.colors)
get_segmentchain_coordinate() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_segmentchain_file_parser() (in module plastid.util.scriptlib.argparsers)
get_segmentchains_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.AnnotationParser method)
(plastid.util.scriptlib.argparsers.MaskParser method)
(plastid.util.scriptlib.argparsers.SequenceParser method)
get_seqdict_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.SequenceParser method)
get_sequence() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_sequence_file_parser() (in module plastid.util.scriptlib.argparsers)
get_short_name() (in module plastid.util.io.openers)
get_str_from_rgb() (in module plastid.plotting.colors)
get_str_from_rgb255() (in module plastid.plotting.colors)
get_subchain() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_transcripts_from_args() (in module plastid.util.scriptlib.argparsers)
(plastid.util.scriptlib.argparsers.AnnotationParser method)
(plastid.util.scriptlib.argparsers.MaskParser method)
(plastid.util.scriptlib.argparsers.SequenceParser method)
get_unstranded() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
get_utr3() (plastid.genomics.roitools.Transcript method)
get_utr5() (plastid.genomics.roitools.Transcript method)
GFF3_Reader (class in plastid.readers.gff)
GFF3_TranscriptAssembler (class in plastid.readers.gff)
group_regions_make_windows() (in module plastid.bin.metagene)
GTF2_Reader (class in plastid.readers.gff)
GTF2_TranscriptAssembler (class in plastid.readers.gff)
guess_formatter() (in module plastid.util.services.misc)
H
half-open
high-throughput sequencing
I
in_separate_process() (in module plastid.util.services.decorators)
indexed file format
indexed_fields (plastid.readers.bigbed.BigBedReader attribute)
isatty() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
iterchroms() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
IUPAC_TABLE (in module plastid.genomics.seqtools)
J
junction_pat (in module plastid.genomics.splicing)
K
k-mer
kde_plot() (in module plastid.plotting.plots)
keys() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
L
length (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
lengths() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
lighten() (in module plastid.plotting.colors)
like() (plastid.genomics.genome_array.GenomeArray static method)
(plastid.genomics.genome_array.SparseGenomeArray static method)
link_pattern (in module plastid.util.scriptlib.help_formatters)
M
ma_plot() (in module plastid.plotting.plots)
main() (in module plastid.bin.counts_in_region)
(in module plastid.bin.crossmap)
(in module plastid.bin.cs)
(in module plastid.bin.findjuncs)
(in module plastid.bin.get_count_vectors)
(in module plastid.bin.gff_parent_types)
(in module plastid.bin.make_wiggle)
(in module plastid.bin.metagene)
(in module plastid.bin.phase_by_size)
(in module plastid.bin.psite)
(in module plastid.bin.reformat_transcripts)
(in module plastid.bin.slidejuncs)
(in module plastid.bin.test_table_equality)
(in module plastid.util.scriptlib.template)
make_GFF3_tokens() (in module plastid.readers.gff_tokens)
make_GTF2_tokens() (in module plastid.readers.gff_tokens)
MalformedFileError
mapping function
mapping rule
mask annotation file
mask file
mask_comments() (plastid.readers.autosql.AutoSqlDeclaration static method)
(plastid.readers.autosql.AutoSqlField static method)
(plastid.readers.autosql.SizedAutoSqlField static method)
(plastid.readers.autosql.ValuesAutoSqlField static method)
mask_segments (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
masked_length (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
MaskParser (class in plastid.util.scriptlib.argparsers)
match_pattern (plastid.readers.autosql.AutoSqlDeclaration attribute)
(plastid.readers.autosql.AutoSqlField attribute)
(plastid.readers.autosql.SizedAutoSqlField attribute)
(plastid.readers.autosql.ValuesAutoSqlField attribute)
match_str (plastid.readers.autosql.AutoSqlDeclaration attribute)
(plastid.readers.autosql.AutoSqlField attribute)
(plastid.readers.autosql.SizedAutoSqlField attribute)
(plastid.readers.autosql.ValuesAutoSqlField attribute)
matches() (plastid.readers.autosql.AutoSqlDeclaration class method)
(plastid.readers.autosql.AutoSqlField class method)
(plastid.readers.autosql.SizedAutoSqlField class method)
(plastid.readers.autosql.ValuesAutoSqlField class method)
maximal spanning window
maximal_spanning_window() (in module plastid.bin.metagene)
merge_genes() (in module plastid.bin.cs)
merge_segments() (in module plastid.genomics.roitools)
merge_sets() (in module plastid.util.services.sets)
metagene
metagene average
module
plastid
plastid.bin
plastid.bin.counts_in_region
plastid.bin.crossmap
plastid.bin.cs
plastid.bin.findjuncs
plastid.bin.get_count_vectors
plastid.bin.gff_parent_types
plastid.bin.make_wiggle
plastid.bin.metagene
plastid.bin.phase_by_size
plastid.bin.psite
plastid.bin.reformat_transcripts
plastid.bin.slidejuncs
plastid.bin.test_table_equality
plastid.genomics
plastid.genomics.c_common
plastid.genomics.genome_array
plastid.genomics.genome_hash
plastid.genomics.map_factories
plastid.genomics.roitools
plastid.genomics.seqtools
plastid.genomics.splicing
plastid.plotting
plastid.plotting.colors
plastid.plotting.plots
plastid.plotting.plotutils
plastid.readers
plastid.readers.autosql
plastid.readers.bbifile
plastid.readers.bed
plastid.readers.bigbed
plastid.readers.bigwig
plastid.readers.bowtie
plastid.readers.common
plastid.readers.gff
plastid.readers.gff_tokens
plastid.readers.psl
plastid.readers.wiggle
plastid.util
plastid.util.io
plastid.util.io.binary
plastid.util.io.filters
plastid.util.io.openers
plastid.util.scriptlib
plastid.util.scriptlib.argparsers
plastid.util.scriptlib.help_formatters
plastid.util.scriptlib.template
plastid.util.services
plastid.util.services.decorators
plastid.util.services.exceptions
plastid.util.services.lists
plastid.util.services.mini2to3
plastid.util.services.misc
plastid.util.services.sets
plastid.util.unique_fifo
multimap
multimapping
multiopen() (in module plastid.util.io.openers)
MutableAbstractGenomeArray (class in plastid.genomics.genome_array)
mutate_seqs() (in module plastid.genomics.seqtools)
N
NameDateWriter (class in plastid.util.io.filters)
next() (plastid.bin.crossmap.FastaNameReader method)
(plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.readers.wiggle.WiggleReader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
nibble (plastid.genomics.map_factories.CenterMapFactory attribute)
nonzero() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
notimplemented() (in module plastid.util.services.decorators)
notused() (in module plastid.util.services.decorators)
NullWriter (class in plastid.util.io.openers)
num_chroms (plastid.readers.bigbed.BigBedReader attribute)
num_records (plastid.readers.bigbed.BigBedReader attribute)
number() (in module plastid.util.services.misc)
O
offset (plastid.genomics.map_factories.FivePrimeMapFactory attribute)
(plastid.genomics.map_factories.ThreePrimeMapFactory attribute)
opener() (in module plastid.util.io.openers)
overlaps() (plastid.genomics.roitools.GenomicSegment method)
(plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
P
P-site offset
paired-end sequencing
parallelize() (in module plastid.util.services.decorators)
parse_GFF3_tokens() (in module plastid.readers.gff_tokens)
parse_GTF2_tokens() (in module plastid.readers.gff_tokens)
parse_list() (in module plastid.util.services.lists)
Parser (class in plastid.util.scriptlib.argparsers)
phase_plot() (in module plastid.plotting.plots)
pl_filters (in module plastid.util.services.exceptions)
pl_once_registry (in module plastid.util.services.exceptions)
plastid
module
plastid.bin
module
plastid.bin.counts_in_region
module
plastid.bin.crossmap
module
plastid.bin.cs
module
plastid.bin.findjuncs
module
plastid.bin.get_count_vectors
module
plastid.bin.gff_parent_types
module
plastid.bin.make_wiggle
module
plastid.bin.metagene
module
plastid.bin.phase_by_size
module
plastid.bin.psite
module
plastid.bin.reformat_transcripts
module
plastid.bin.slidejuncs
module
plastid.bin.test_table_equality
module
plastid.genomics
module
plastid.genomics.c_common
module
plastid.genomics.genome_array
module
plastid.genomics.genome_hash
module
plastid.genomics.map_factories
module
plastid.genomics.roitools
module
plastid.genomics.seqtools
module
plastid.genomics.splicing
module
plastid.plotting
module
plastid.plotting.colors
module
plastid.plotting.plots
module
plastid.plotting.plotutils
module
plastid.readers
module
plastid.readers.autosql
module
plastid.readers.bbifile
module
plastid.readers.bed
module
plastid.readers.bigbed
module
plastid.readers.bigwig
module
plastid.readers.bowtie
module
plastid.readers.common
module
plastid.readers.gff
module
plastid.readers.gff_tokens
module
plastid.readers.psl
module
plastid.readers.wiggle
module
plastid.util
module
plastid.util.io
module
plastid.util.io.binary
module
plastid.util.io.filters
module
plastid.util.io.openers
module
plastid.util.scriptlib
module
plastid.util.scriptlib.argparsers
module
plastid.util.scriptlib.help_formatters
module
plastid.util.scriptlib.template
module
plastid.util.services
module
plastid.util.services.decorators
module
plastid.util.services.exceptions
module
plastid.util.services.lists
module
plastid.util.services.mini2to3
module
plastid.util.services.misc
module
plastid.util.services.sets
module
plastid.util.unique_fifo
module
plastid_default_scatter (in module plastid.plotting.plots)
plot() (plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
PlottingParser (class in plastid.util.scriptlib.argparsers)
positionlist_to_segments() (in module plastid.genomics.roitools)
positions_to_segments() (in module plastid.genomics.roitools)
PrefixNamespaceWrapper (class in plastid.util.scriptlib.argparsers)
pretty_print_dict() (in module plastid.util.io.openers)
Printer (in module plastid.util.io.filters)
process_partial_group() (in module plastid.bin.cs)
profile_heatmap() (in module plastid.plotting.plots)
PSL_Reader (class in plastid.readers.psl)
pyrst_pattern (in module plastid.util.scriptlib.help_formatters)
Python Enhancement Proposals
PEP 257
PEP 440
PEP 479
PEP 8
R
random_seq() (in module plastid.genomics.seqtools)
read alignments
read() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
read_pl_table() (in module plastid.util.io.openers)
readable() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
readline() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
readlines() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
region of interest
remove_filter() (plastid.genomics.genome_array.BAMGenomeArray method)
reset_masks() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
reset_sum() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
return_type (plastid.readers.bigbed.BigBedReader attribute)
revcomp_mask_chain() (in module plastid.bin.crossmap)
revive() (in module plastid.genomics.seqtools)
ribosome profiling
ribosome-protected footprint
roi
roi_row_to_cds() (in module plastid.bin.phase_by_size)
row_keys (plastid.genomics.map_factories.StratifiedVariableFivePrimeMapFactory attribute)
RPKM
S
safe_bytes() (in module plastid.util.services.mini2to3)
safe_str() (in module plastid.util.services.mini2to3)
scatterhist_x() (in module plastid.plotting.plots)
scatterhist_xy() (in module plastid.plotting.plots)
scatterhist_y() (in module plastid.plotting.plots)
search() (plastid.readers.bigbed.BigBedReader method)
seek() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
seekable() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
SegmentChain (class in plastid.genomics.roitools)
segments (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
seq_to_regex() (in module plastid.genomics.seqtools)
SequenceParser (class in plastid.util.scriptlib.argparsers)
set_mapping() (plastid.genomics.genome_array.BAMGenomeArray method)
set_normalize() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
set_style_from_args() (plastid.util.scriptlib.argparsers.PlottingParser method)
set_sum() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
shape (plastid.genomics.map_factories.StratifiedVariableFivePrimeMapFactory attribute)
shares_segments_with() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
shorten_help() (in module plastid.util.scriptlib.help_formatters)
simulate_reads() (in module plastid.bin.crossmap)
single-end sequencing
SizedAutoSqlField (class in plastid.readers.autosql)
SizeFilterFactory (class in plastid.genomics.map_factories)
skip_if_abstract() (in module plastid.util.services.decorators)
SkipBlankReader (class in plastid.util.io.filters)
skipdoc() (in module plastid.util.services.decorators)
sort() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
sort_max_position() (in module plastid.plotting.plots)
spanning_segment (plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
SparseGenomeArray (class in plastid.genomics.genome_array)
split_axes() (in module plastid.plotting.plotutils)
stacked_bar() (in module plastid.plotting.plots)
start (plastid.genomics.roitools.GenomicSegment attribute)
start codon peak
stop codon peak
StopFeature (in module plastid.readers.gff)
strand (plastid.genomics.roitools.GenomicSegment attribute)
(plastid.genomics.roitools.SegmentChain attribute)
(plastid.genomics.roitools.Transcript attribute)
strands() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
StratifiedVariableFivePrimeMapFactory (class in plastid.genomics.map_factories)
sub-codon phasing
subst_pattern (in module plastid.util.scriptlib.help_formatters)
sum() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.MutableAbstractGenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
(plastid.readers.bigwig.BigWigReader method)
T
TabixGenomeHash (class in plastid.genomics.genome_hash)
TeeListener (class in plastid.util.io.filters)
TeeReader (class in plastid.util.io.filters)
tell() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
test_dataframe_equality() (in module plastid.bin.test_table_equality)
TestTeeListener (class in plastid.util.io.filters)
three_prime_map() (in module plastid.genomics.genome_array)
ThreePrimeMapFactory (class in plastid.genomics.map_factories)
to_bedgraph() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
to_genome_array() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.BigWigGenomeArray method)
to_variable_step() (plastid.genomics.genome_array.BAMGenomeArray method)
(plastid.genomics.genome_array.GenomeArray method)
(plastid.genomics.genome_array.SparseGenomeArray method)
Transcript (class in plastid.genomics.roitools)
translation efficiency
triangle_plot() (in module plastid.plotting.plots)
trianglize() (in module plastid.plotting.plots)
triplet periodicity
truncate() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
TwoBitSeqRecordAdaptor (class in plastid.genomics.seqtools)
U
uncompress_buf_size (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
unescape() (in module plastid.readers.gff_tokens)
unescape_GFF3() (in module plastid.readers.gff_tokens)
unescape_GTF2() (in module plastid.readers.gff_tokens)
UniqueFIFO (class in plastid.util.unique_fifo)
unstranded_overlaps() (plastid.genomics.roitools.SegmentChain method)
(plastid.genomics.roitools.Transcript method)
update() (plastid.genomics.genome_hash.GenomeHash method)
V
ValuesAutoSqlField (class in plastid.readers.autosql)
variable_five_prime_map() (in module plastid.genomics.genome_array)
VariableFivePrimeMapFactory (class in plastid.genomics.map_factories)
version (plastid.readers.bigbed.BigBedReader attribute)
(plastid.readers.bigwig.BigWigReader attribute)
W
warn() (in module plastid.util.services.exceptions)
warn_explicit() (in module plastid.util.services.exceptions)
warn_explicit_onceperfamily() (in module plastid.util.services.exceptions)
warn_onceperfamily() (in module plastid.util.services.exceptions)
WiggleReader (class in plastid.readers.wiggle)
window_cds_start() (in module plastid.bin.metagene)
window_cds_stop() (in module plastid.bin.metagene)
window_landmark() (in module plastid.bin.metagene)
with_traceback() (plastid.util.services.exceptions.ArgumentWarning method)
(plastid.util.services.exceptions.DataWarning method)
(plastid.util.services.exceptions.FileFormatWarning method)
(plastid.util.services.exceptions.MalformedFileError method)
writable() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
write() (plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.openers.NullWriter method)
write_pl_table() (in module plastid.util.io.openers)
writelines() (plastid.bin.crossmap.FastaNameReader method)
(plastid.readers.bed.BED_Reader method)
(plastid.readers.bowtie.BowtieReader method)
(plastid.readers.common.AssembledFeatureReader method)
(plastid.readers.gff.GFF3_Reader method)
(plastid.readers.gff.GFF3_TranscriptAssembler method)
(plastid.readers.gff.GTF2_Reader method)
(plastid.readers.gff.GTF2_TranscriptAssembler method)
(plastid.readers.psl.BundledPSL_Reader method)
(plastid.readers.psl.PSL_Reader method)
(plastid.util.io.filters.BackwardReader method)
(plastid.util.io.filters.ColorWriter method)
(plastid.util.io.filters.CommentReader method)
(plastid.util.io.filters.CommentWriter method)
(plastid.util.io.filters.FunctionReader method)
(plastid.util.io.filters.NameDateWriter method)
(plastid.util.io.filters.SkipBlankReader method)
(plastid.util.io.filters.TeeReader method)
(plastid.util.io.openers.NullWriter method)
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