ngs-tools
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API
ngs-tools
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Index
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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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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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Q
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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
_
_10X_ATAC (in module ngs_tools.chemistry.SingleCellChemistry)
_10X_FB (in module ngs_tools.chemistry.SingleCellChemistry)
_10X_FEATUREBARCODE (in module ngs_tools.chemistry.MultimodalChemistry)
_10X_MULTIOME (in module ngs_tools.chemistry.MultimodalChemistry)
_10X_V1 (in module ngs_tools.chemistry.SingleCellChemistry)
_10X_V2 (in module ngs_tools.chemistry.SingleCellChemistry)
_10X_V3 (in module ngs_tools.chemistry.SingleCellChemistry)
_10X_V3_ULTIMA (in module ngs_tools.chemistry.SingleCellChemistry)
__and__() (ngs_tools.binary.ArgumentValidator.ArgumentValidator method)
__bool__() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
__call__() (ngs_tools.binary.ArgumentValidator.AndValidator method)
(ngs_tools.binary.ArgumentValidator.ArgumentValidator method)
(ngs_tools.binary.ArgumentValidator.ConstantValidator method)
(ngs_tools.binary.ArgumentValidator.DirValidator method)
(ngs_tools.binary.ArgumentValidator.FileValidator method)
(ngs_tools.binary.ArgumentValidator.FloatValidator method)
(ngs_tools.binary.ArgumentValidator.IntegerValidator method)
(ngs_tools.binary.ArgumentValidator.NotValidator method)
(ngs_tools.binary.ArgumentValidator.NoValidator method)
(ngs_tools.binary.ArgumentValidator.OrValidator method)
(ngs_tools.binary.ArgumentValidator.PositiveValidator method)
(ngs_tools.binary.Binary.Binary method)
(ngs_tools.binary.Binary.BinaryExecutor method)
(ngs_tools.utils.ParallelWithProgress method)
__del__() (ngs_tools.utils.FileWrapper method)
__enter__() (ngs_tools.utils.FileWrapper method)
(ngs_tools.utils.suppress_stdout_stderr method)
__eq__() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
(ngs_tools.chemistry.Chemistry.SubSequenceDefinition method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
__exit__() (ngs_tools.utils.FileWrapper method)
(ngs_tools.utils.suppress_stdout_stderr method)
__getitem__() (ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.fastq.Read.Quality method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
__gt__() (ngs_tools.gtf.Segment.Segment method)
__invert__() (ngs_tools.binary.ArgumentValidator.ArgumentValidator method)
__iter__() (ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
(ngs_tools.utils.FileWrapper method)
__len__() (ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
__lt__() (ngs_tools.gtf.Segment.Segment method)
__or__() (ngs_tools.binary.ArgumentValidator.ArgumentValidator method)
__repr__() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
(ngs_tools.chemistry.Chemistry.SubSequenceDefinition method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
__str__() (ngs_tools.binary.ArgumentValidator.AndValidator method)
(ngs_tools.binary.ArgumentValidator.ArgumentValidator method)
(ngs_tools.binary.ArgumentValidator.ConstantValidator method)
(ngs_tools.binary.ArgumentValidator.DirValidator method)
(ngs_tools.binary.ArgumentValidator.FileValidator method)
(ngs_tools.binary.ArgumentValidator.FloatValidator method)
(ngs_tools.binary.ArgumentValidator.IntegerValidator method)
(ngs_tools.binary.ArgumentValidator.NotValidator method)
(ngs_tools.binary.ArgumentValidator.NoValidator method)
(ngs_tools.binary.ArgumentValidator.OrValidator method)
(ngs_tools.binary.ArgumentValidator.PositiveValidator method)
(ngs_tools.binary.Binary.Binary method)
(ngs_tools.chemistry.Chemistry.SequencingChemistry method)
(ngs_tools.chemistry.Chemistry.SubSequenceDefinition method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
__version__ (in module ngs_tools)
_attribute_str (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
_BDWTA (in module ngs_tools.chemistry.SingleCellChemistry)
_calculate_positional_probs() (in module ngs_tools.sequence)
_CELSEQ_V1 (in module ngs_tools.chemistry.SingleCellChemistry)
_CELSEQ_V2 (in module ngs_tools.chemistry.SingleCellChemistry)
_chromosome (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
_clean_name() (in module ngs_tools.chemistry)
_correct_to_whitelist() (in module ngs_tools.sequence)
_COSMX (in module ngs_tools.chemistry.SpatialChemistry)
_definitions (ngs_tools.chemistry.Chemistry.SubSequenceParser attribute)
_description (ngs_tools.chemistry.Chemistry.Chemistry attribute)
_disambiguate_sequence() (in module ngs_tools.sequence)
_DROPLET_SINGLE_CELL_CHEMISTRIES (in module ngs_tools.chemistry.SingleCellChemistry)
_DROPSEQ (in module ngs_tools.chemistry.SingleCellChemistry)
_end (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
(ngs_tools.gtf.Segment.Segment attribute)
_feature (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
_files (ngs_tools.chemistry.Chemistry.Chemistry attribute)
_hamming_distance() (in module ngs_tools.sequence)
_hamming_distance_matrix() (in module ngs_tools.sequence)
_hamming_distances() (in module ngs_tools.sequence)
_header (ngs_tools.fasta.Fasta.Fasta attribute)
(ngs_tools.fasta.FastaEntry.FastaEntry attribute)
(ngs_tools.fastq.Read.Read attribute)
_index (ngs_tools.chemistry.Chemistry.SubSequenceDefinition attribute)
_INDROPS_V1 (in module ngs_tools.chemistry.SingleCellChemistry)
_INDROPS_V2 (in module ngs_tools.chemistry.SingleCellChemistry)
_INDROPS_V3 (in module ngs_tools.chemistry.SingleCellChemistry)
_INSITU_SPATIAL_CHEMISTRIES (in module ngs_tools.chemistry.SpatialChemistry)
_length (ngs_tools.chemistry.Chemistry.SubSequenceDefinition attribute)
_line (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
_MERFISH (in module ngs_tools.chemistry.SpatialChemistry)
_mismatch_mask() (in module ngs_tools.sequence)
_mismatch_masks() (in module ngs_tools.sequence)
_most_likely_array() (in module ngs_tools.sequence)
_most_likely_sequence() (in module ngs_tools.sequence)
_name (ngs_tools.chemistry.Chemistry.Chemistry attribute)
_open() (ngs_tools.utils.FileWrapper method)
_OTHER_SINGLE_CELL_CHEMISTRIES (in module ngs_tools.chemistry.SingleCellChemistry)
_pairwise_hamming_distances() (in module ngs_tools.sequence)
_PLATE_SINGLE_CELL_CHEMISTRIES (in module ngs_tools.chemistry.SingleCellChemistry)
_qualities (ngs_tools.fastq.Read.Read attribute)
_qualities_to_array() (in module ngs_tools.sequence)
_SCI_FATE (in module ngs_tools.chemistry.SingleCellChemistry)
_SCRBSEQ (in module ngs_tools.chemistry.SingleCellChemistry)
_segments (ngs_tools.gtf.SegmentCollection.SegmentCollection attribute)
_SEQFISH (in module ngs_tools.chemistry.SpatialChemistry)
_SEQSCOPE_HDMI32_DRA1 (in module ngs_tools.chemistry.SpatialChemistry)
_SEQSCOPE_HDMI_DRAI (in module ngs_tools.chemistry.SpatialChemistry)
_sequence (ngs_tools.fasta.FastaEntry.FastaEntry attribute)
(ngs_tools.fastq.Read.Read attribute)
_sequence_to_array() (in module ngs_tools.sequence)
_SEQUENCING_SPATIAL_CHEMISTRIES (in module ngs_tools.chemistry.SpatialChemistry)
_SLIDESEQ_V2 (in module ngs_tools.chemistry.SpatialChemistry)
_SMARTSEQ_V2 (in module ngs_tools.chemistry.SingleCellChemistry)
_SMARTSEQ_V3 (in module ngs_tools.chemistry.SingleCellChemistry)
_SPLITSEQ (in module ngs_tools.chemistry.SingleCellChemistry)
_STARMAP (in module ngs_tools.chemistry.SpatialChemistry)
_start (ngs_tools.chemistry.Chemistry.SubSequenceDefinition attribute)
(ngs_tools.gtf.GtfEntry.GtfEntry attribute)
(ngs_tools.gtf.Segment.Segment attribute)
_STEREOSEQ (in module ngs_tools.chemistry.SpatialChemistry)
_STORMSEQ (in module ngs_tools.chemistry.SingleCellChemistry)
_strand (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
_string (ngs_tools.fastq.Read.Quality attribute)
_SURECELL (in module ngs_tools.chemistry.SingleCellChemistry)
_VISIUM (in module ngs_tools.chemistry.SpatialChemistry)
A
add_collection() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
add_segment() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
addHandler() (ngs_tools.logging.Logger method)
alignment_to_cigar() (in module ngs_tools.sequence)
all_exists() (in module ngs_tools.utils)
AndValidator (class in ngs_tools.binary.ArgumentValidator)
apply_bam() (in module ngs_tools.bam)
Argument (class in ngs_tools.binary.Argument)
ArgumentError
ArgumentValidator (class in ngs_tools.binary.ArgumentValidator)
ATTRIBUTE_PARSER (ngs_tools.fasta.FastaEntry.FastaEntry attribute)
,
[1]
(ngs_tools.gtf.GtfEntry.GtfEntry attribute)
,
[1]
attributes (ngs_tools.fasta.FastaEntry.FastaEntry property)
(ngs_tools.fastq.Read.Read property)
(ngs_tools.gtf.GtfEntry.GtfEntry property)
B
BamError
barcode_parser (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
Binary (class in ngs_tools.binary.Binary)
BinaryError
BinaryExecutor (class in ngs_tools.binary.Binary)
BinaryResult (class in ngs_tools.binary.Binary)
C
call_consensus() (in module ngs_tools.sequence)
call_consensus_with_qualities() (in module ngs_tools.sequence)
cdna_parser (ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
cell_barcode_parser (ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
ch (ngs_tools.logging.Logger attribute)
CHEMISTRIES (in module ngs_tools.chemistry)
chemistries (ngs_tools.chemistry.MultimodalChemistry.MultimodalChemistry property)
Chemistry (class in ngs_tools.chemistry.Chemistry)
chemistry() (ngs_tools.chemistry.MultimodalChemistry.MultimodalChemistry method)
ChemistryError
chromosome (ngs_tools.gtf.GtfEntry.GtfEntry property)
close() (ngs_tools.utils.FileWrapper method)
closed (ngs_tools.utils.FileWrapper attribute)
(ngs_tools.utils.FileWrapper property)
collapse() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
command (ngs_tools.binary.Binary.BinaryResult attribute)
complement_sequence() (in module ngs_tools.sequence)
compress_gzip() (in module ngs_tools.utils)
concatenate_files() (in module ngs_tools.utils)
concatenate_files_as_text() (in module ngs_tools.utils)
ConstantArgument (class in ngs_tools.binary.Argument)
ConstantValidator (class in ngs_tools.binary.ArgumentValidator)
correct_sequences_to_whitelist() (in module ngs_tools.sequence)
correct_sequences_to_whitelist_simple() (in module ngs_tools.sequence)
count_bam() (in module ngs_tools.bam)
critical() (ngs_tools.logging.Logger method)
D
debug() (ngs_tools.logging.Logger method)
decompress_gzip() (in module ngs_tools.utils)
definitions (ngs_tools.chemistry.Chemistry.SubSequenceParser property)
description (ngs_tools.chemistry.Chemistry.Chemistry property)
(ngs_tools.chemistry.MultimodalChemistry.MultimodalChemistry property)
DirValidator (class in ngs_tools.binary.ArgumentValidator)
download_file() (in module ngs_tools.utils)
E
end (ngs_tools.chemistry.Chemistry.SubSequenceDefinition property)
(ngs_tools.gtf.GtfEntry.GtfEntry property)
(ngs_tools.gtf.Segment.Segment property)
(ngs_tools.gtf.SegmentCollection.SegmentCollection property)
error() (ngs_tools.logging.Logger method)
exception() (ngs_tools.logging.Logger method)
F
Fasta (class in ngs_tools.fasta.Fasta)
FastaEntry (class in ngs_tools.fasta.FastaEntry)
FastaEntryError
FastaError
Fastq (class in ngs_tools.fastq.Fastq)
fastq_to_bam() (in module ngs_tools.fastq)
FastqError
fastqs_to_bam() (in module ngs_tools.fastq)
fastqs_to_bam_with_chemistry() (in module ngs_tools.fastq)
feature (ngs_tools.gtf.GtfEntry.GtfEntry property)
FileValidator (class in ngs_tools.binary.ArgumentValidator)
FileWrapper (class in ngs_tools.utils)
filter_bam() (in module ngs_tools.bam)
flank() (ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
flatten_dict_values() (in module ngs_tools.utils)
flatten_dictionary() (in module ngs_tools.utils)
flatten_iter() (in module ngs_tools.utils)
FloatValidator (class in ngs_tools.binary.ArgumentValidator)
FORMAT (ngs_tools.logging.Logger attribute)
,
[1]
FORWARD (ngs_tools.chemistry.Chemistry.SequencingStrand attribute)
fp (ngs_tools.utils.FileWrapper attribute)
from_collections() (ngs_tools.gtf.SegmentCollection.SegmentCollection class method)
from_positions() (ngs_tools.gtf.SegmentCollection.SegmentCollection class method)
G
genes_and_transcripts_from_gtf() (in module ngs_tools.gtf)
get_chemistry() (in module ngs_tools.chemistry)
get_file() (ngs_tools.chemistry.Chemistry.Chemistry method)
get_parser() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
Gtf (class in ngs_tools.gtf.Gtf)
GtfEntry (class in ngs_tools.gtf.GtfEntry)
GtfEntryError
GtfError
H
hamming_distance() (in module ngs_tools.sequence)
hamming_distance_matrix() (in module ngs_tools.sequence)
hamming_distances() (in module ngs_tools.sequence)
has_barcode (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
has_cell_barcode (ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
has_file() (ngs_tools.chemistry.Chemistry.Chemistry method)
has_parser() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
has_spot_barcode (ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
has_umi (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
has_whitelist (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
header (ngs_tools.fasta.FastaEntry.FastaEntry property)
(ngs_tools.fastq.Read.Read property)
I
index (ngs_tools.chemistry.Chemistry.SubSequenceDefinition property)
info() (ngs_tools.logging.Logger method)
IntegerValidator (class in ngs_tools.binary.ArgumentValidator)
invert() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
is_exclusive() (ngs_tools.gtf.Segment.Segment method)
is_gzip (ngs_tools.utils.FileWrapper property)
is_gzip() (in module ngs_tools.utils)
is_in() (ngs_tools.gtf.Segment.Segment method)
is_overlapping() (ngs_tools.chemistry.Chemistry.SubSequenceDefinition method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
(ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
is_remote (ngs_tools.utils.FileWrapper property)
is_remote() (in module ngs_tools.utils)
is_subset() (ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
is_superset() (ngs_tools.gtf.Segment.Segment method)
(ngs_tools.gtf.SegmentCollection.SegmentCollection method)
IsDir (in module ngs_tools.binary.ArgumentValidator)
IsFile (in module ngs_tools.binary.ArgumentValidator)
IsFloat (in module ngs_tools.binary.ArgumentValidator)
IsInteger (in module ngs_tools.binary.ArgumentValidator)
IsPositive (in module ngs_tools.binary.ArgumentValidator)
IsPositiveInteger (in module ngs_tools.binary.ArgumentValidator)
L
length (ngs_tools.chemistry.Chemistry.SubSequenceDefinition property)
lengths (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
levenshtein_distance() (in module ngs_tools.sequence)
LEVENSHTEIN_DISTANCE_ALIGNER (in module ngs_tools.sequence)
line (ngs_tools.gtf.GtfEntry.GtfEntry property)
Logger (class in ngs_tools.logging)
logger (in module ngs_tools.logging)
(ngs_tools.logging.Logger attribute)
M
make_header() (ngs_tools.fasta.FastaEntry.FastaEntry static method)
map_bam() (in module ngs_tools.bam)
MASK_TO_NUCLEOTIDE (in module ngs_tools.sequence)
merge_dictionaries() (in module ngs_tools.utils)
mkstemp() (in module ngs_tools.utils)
mode (ngs_tools.utils.FileWrapper attribute)
module
ngs_tools
ngs_tools.bam
ngs_tools.binary
ngs_tools.binary.Argument
ngs_tools.binary.ArgumentValidator
ngs_tools.binary.Binary
ngs_tools.chemistry
ngs_tools.chemistry.Chemistry
ngs_tools.chemistry.MultimodalChemistry
ngs_tools.chemistry.SingleCellChemistry
ngs_tools.chemistry.SpatialChemistry
ngs_tools.fasta
ngs_tools.fasta.Fasta
ngs_tools.fasta.FastaEntry
ngs_tools.fastq
ngs_tools.fastq.Fastq
ngs_tools.fastq.Read
ngs_tools.gtf
ngs_tools.gtf.Gtf
ngs_tools.gtf.GtfEntry
ngs_tools.gtf.Segment
ngs_tools.gtf.SegmentCollection
ngs_tools.logging
ngs_tools.progress
ngs_tools.sequence
ngs_tools.utils
MULTIMODAL_CHEMISTRIES (in module ngs_tools.chemistry.MultimodalChemistry)
MultimodalChemistry (class in ngs_tools.chemistry.MultimodalChemistry)
MultimodalChemistryError
N
n (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
name (ngs_tools.binary.Argument.Argument property)
(ngs_tools.chemistry.Chemistry.Chemistry property)
(ngs_tools.chemistry.MultimodalChemistry.MultimodalChemistry property)
(ngs_tools.fasta.FastaEntry.FastaEntry property)
(ngs_tools.fastq.Read.Read property)
NamedArgument (class in ngs_tools.binary.Argument)
namespace_message() (ngs_tools.logging.Logger method)
namespaced() (ngs_tools.logging.Logger method)
namespaced_context() (ngs_tools.logging.Logger method)
NeedlemanWunsch (in module ngs_tools.sequence)
ngs_tools
module
ngs_tools.bam
module
ngs_tools.binary
module
ngs_tools.binary.Argument
module
ngs_tools.binary.ArgumentValidator
module
ngs_tools.binary.Binary
module
ngs_tools.chemistry
module
ngs_tools.chemistry.Chemistry
module
ngs_tools.chemistry.MultimodalChemistry
module
ngs_tools.chemistry.SingleCellChemistry
module
ngs_tools.chemistry.SpatialChemistry
module
ngs_tools.fasta
module
ngs_tools.fasta.Fasta
module
ngs_tools.fasta.FastaEntry
module
ngs_tools.fastq
module
ngs_tools.fastq.Fastq
module
ngs_tools.fastq.Read
module
ngs_tools.gtf
module
ngs_tools.gtf.Gtf
module
ngs_tools.gtf.GtfEntry
module
ngs_tools.gtf.Segment
module
ngs_tools.gtf.SegmentCollection
module
ngs_tools.logging
module
ngs_tools.progress
module
ngs_tools.sequence
module
ngs_tools.utils
module
NotValidator (class in ngs_tools.binary.ArgumentValidator)
NoValidator (class in ngs_tools.binary.ArgumentValidator)
NUCLEOTIDE_COMPLEMENT (in module ngs_tools.sequence)
NUCLEOTIDE_MASKS (in module ngs_tools.sequence)
NUCLEOTIDES (in module ngs_tools.sequence)
NUCLEOTIDES_AMBIGUOUS (in module ngs_tools.sequence)
NUCLEOTIDES_PERMISSIVE (in module ngs_tools.sequence)
NUCLEOTIDES_STRICT (in module ngs_tools.sequence)
O
open_as_text() (in module ngs_tools.utils)
OrValidator (class in ngs_tools.binary.ArgumentValidator)
P
pairwise_hamming_distances() (in module ngs_tools.sequence)
ParallelWithProgress (class in ngs_tools.utils)
parse() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
(ngs_tools.chemistry.Chemistry.SubSequenceDefinition method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
parse_gtf() (in module ngs_tools.gtf)
parse_reads() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
(ngs_tools.chemistry.Chemistry.SubSequenceParser method)
PARSER (ngs_tools.gtf.GtfEntry.GtfEntry attribute)
,
[1]
parsers (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
path (ngs_tools.binary.Binary.Binary property)
(ngs_tools.utils.FileWrapper attribute)
PositionalArgument (class in ngs_tools.binary.Argument)
PositiveValidator (class in ngs_tools.binary.ArgumentValidator)
post_execute() (ngs_tools.binary.Argument.Argument method)
(ngs_tools.binary.Binary.Binary method)
(ngs_tools.binary.Binary.BinaryExecutor method)
pre_execute() (ngs_tools.binary.Argument.Argument method)
(ngs_tools.binary.Binary.Binary method)
(ngs_tools.binary.Binary.BinaryExecutor method)
print_progress() (ngs_tools.utils.ParallelWithProgress method)
probs (ngs_tools.fastq.Read.Quality property)
process (ngs_tools.binary.Binary.BinaryResult attribute)
progress (in module ngs_tools.progress)
Q
qualities (ngs_tools.fastq.Read.Read property)
Quality (class in ngs_tools.fastq.Read)
R
Read (class in ngs_tools.fastq.Read)
read() (ngs_tools.fasta.Fasta.Fasta method)
(ngs_tools.fastq.Fastq.Fastq method)
(ngs_tools.gtf.Gtf.Gtf method)
(ngs_tools.utils.FileWrapper method)
read_pickle() (in module ngs_tools.utils)
ReadError
removeHandler() (ngs_tools.logging.Logger method)
render() (ngs_tools.binary.Argument.Argument method)
(ngs_tools.binary.Argument.ConstantArgument method)
(ngs_tools.binary.Argument.NamedArgument method)
reorder() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
required (ngs_tools.binary.Argument.Argument property)
reset() (ngs_tools.utils.FileWrapper method)
resolution (ngs_tools.chemistry.SpatialChemistry.SpatialChemistry property)
retry() (in module ngs_tools.utils)
retry_decorator() (in module ngs_tools.utils)
REVERSE (ngs_tools.chemistry.Chemistry.SequencingStrand attribute)
run_executable() (in module ngs_tools.utils)
S
scale (ngs_tools.chemistry.SpatialChemistry.SpatialResolution attribute)
Segment (class in ngs_tools.gtf.Segment)
SegmentCollection (class in ngs_tools.gtf.SegmentCollection)
SegmentCollectionError
SegmentError
segments (ngs_tools.gtf.SegmentCollection.SegmentCollection property)
sequence (ngs_tools.fasta.FastaEntry.FastaEntry property)
(ngs_tools.fastq.Read.Read property)
SEQUENCE_PARSER (in module ngs_tools.sequence)
SequenceError
SequencingChemistry (class in ngs_tools.chemistry.Chemistry)
SequencingStrand (class in ngs_tools.chemistry.Chemistry)
set_executable() (in module ngs_tools.utils)
set_logger() (in module ngs_tools.logging)
setLevel() (ngs_tools.logging.Logger method)
silence_logger() (in module ngs_tools.logging)
SINGLE_CELL_CHEMISTRIES (in module ngs_tools.chemistry.SingleCellChemistry)
SingleCellChemistry (class in ngs_tools.chemistry.SingleCellChemistry)
SingleCellChemistryError
span_is_exclusive() (ngs_tools.gtf.SegmentCollection.SegmentCollection method)
SPATIAL_CHEMISTRIES (in module ngs_tools.chemistry.SpatialChemistry)
SpatialChemistry (class in ngs_tools.chemistry.SpatialChemistry)
SpatialChemistryError
SpatialResolution (class in ngs_tools.chemistry.SpatialChemistry)
SpatialSequencingChemistry (class in ngs_tools.chemistry.SpatialChemistry)
split_bam() (in module ngs_tools.bam)
split_genomic_fasta_to_cdna() (in module ngs_tools.fasta)
split_genomic_fasta_to_intron() (in module ngs_tools.fasta)
split_genomic_fasta_to_nascent() (in module ngs_tools.fasta)
spot_barcode_parser (ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
start (ngs_tools.chemistry.Chemistry.SubSequenceDefinition property)
(ngs_tools.gtf.GtfEntry.GtfEntry property)
(ngs_tools.gtf.Segment.Segment property)
(ngs_tools.gtf.SegmentCollection.SegmentCollection property)
stderr (ngs_tools.binary.Binary.BinaryResult attribute)
stdout (ngs_tools.binary.Binary.BinaryResult attribute)
strand (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.gtf.GtfEntry.GtfEntry property)
stream_file() (in module ngs_tools.utils)
string (ngs_tools.fastq.Read.Quality property)
SubSequenceDefinition (class in ngs_tools.chemistry.Chemistry)
SubSequenceDefinitionError
SubSequenceParser (class in ngs_tools.chemistry.Chemistry)
SubSequenceParserError
suppress_stdout_stderr (class in ngs_tools.utils)
T
tag_bam_with_fastq() (in module ngs_tools.bam)
tell() (ngs_tools.utils.FileWrapper method)
to_kallisto_bus_arguments() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
to_segment() (ngs_tools.gtf.GtfEntry.GtfEntry method)
to_starsolo_arguments() (ngs_tools.chemistry.Chemistry.SequencingChemistry method)
TqdmUpTo (class in ngs_tools.utils)
U
umi_parser (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
unit (ngs_tools.chemistry.SpatialChemistry.SpatialResolution attribute)
UNSTRANDED (ngs_tools.chemistry.Chemistry.SequencingStrand attribute)
update_to() (ngs_tools.utils.TqdmUpTo method)
V
values (ngs_tools.fastq.Read.Quality property)
VERSION_PARSER (in module ngs_tools.chemistry)
W
warning() (ngs_tools.logging.Logger method)
whitelist_path (ngs_tools.chemistry.Chemistry.SequencingChemistry property)
(ngs_tools.chemistry.SingleCellChemistry.SingleCellChemistry property)
(ngs_tools.chemistry.SpatialChemistry.SpatialSequencingChemistry property)
WHITELISTS_DIR (in module ngs_tools.chemistry.Chemistry)
width (ngs_tools.gtf.Segment.Segment property)
write() (ngs_tools.fasta.Fasta.Fasta method)
(ngs_tools.fastq.Fastq.Fastq method)
(ngs_tools.gtf.Gtf.Gtf method)
(ngs_tools.utils.FileWrapper method)
write_pickle() (in module ngs_tools.utils)
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