HTSinfer
stable
Modules
htsinfer
HTSinfer
Index
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Index
A
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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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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
A
adapt_3 (htsinfer.models.Layout attribute)
,
[1]
adapter_counts (htsinfer.get_read_layout.GetAdapter3 attribute)
adapter_file (htsinfer.get_read_layout.GetAdapter3 attribute)
(htsinfer.get_read_layout.GetReadLayout attribute)
adapters (htsinfer.get_read_layout.GetAdapter3 attribute)
Args (class in htsinfer.models)
args (htsinfer.models.Config attribute)
,
[1]
C
clean_up() (htsinfer.htsinfer.HtsInfer method)
cleanup_regime (htsinfer.models.Args attribute)
,
[1]
CleanupRegimes (class in htsinfer.models)
Config (class in htsinfer.models)
config (htsinfer.htsinfer.HtsInfer attribute)
convert_dict_to_df() (in module htsinfer.utils)
create_kallisto_index() (htsinfer.get_library_source.GetLibSource method)
create_star_index() (htsinfer.mapping.Mapping method)
CRITICAL (htsinfer.models.LogLevels attribute)
CutadaptProblem
D
DEBUG (htsinfer.models.LogLevels attribute)
DEFAULT (htsinfer.models.CleanupRegimes attribute)
E
ERROR (htsinfer.models.LogLevels attribute)
(htsinfer.models.RunStates attribute)
evaluate() (htsinfer.get_library_source.GetLibSource method)
(htsinfer.get_library_stats.GetLibStats method)
(htsinfer.get_library_type.GetFastqType method)
(htsinfer.get_library_type.GetLibType method)
(htsinfer.get_read_layout.GetAdapter3 method)
(htsinfer.get_read_layout.GetReadLayout method)
(htsinfer.get_read_orientation.GetOrientation method)
(htsinfer.htsinfer.HtsInfer method)
(htsinfer.mapping.Mapping method)
F
fastq_get_stats_read_length() (htsinfer.get_library_stats.GetLibStats static method)
file_1 (htsinfer.models.ResultsLayout attribute)
,
[1]
(htsinfer.models.ResultsOrientation attribute)
,
[1]
(htsinfer.models.ResultsSource attribute)
,
[1]
(htsinfer.models.ResultsStats attribute)
,
[1]
(htsinfer.models.ResultsType attribute)
,
[1]
file_2 (htsinfer.models.ResultsLayout attribute)
,
[1]
(htsinfer.models.ResultsOrientation attribute)
,
[1]
(htsinfer.models.ResultsSource attribute)
,
[1]
(htsinfer.models.ResultsStats attribute)
,
[1]
(htsinfer.models.ResultsType attribute)
,
[1]
file_problem (htsinfer.models.StatesType attribute)
FileProblem
first_mate (htsinfer.models.StatesType attribute)
,
[1]
first_mate_assumed (htsinfer.models.StatesType attribute)
G
generate_star_alignments() (htsinfer.mapping.Mapping static method)
get_fasta_size() (htsinfer.mapping.Mapping static method)
get_frequencies() (htsinfer.get_read_orientation.GetOrientation static method)
get_library_source() (htsinfer.htsinfer.HtsInfer method)
get_library_stats() (htsinfer.htsinfer.HtsInfer method)
get_library_type() (htsinfer.htsinfer.HtsInfer method)
get_poly_a() (htsinfer.get_read_layout.GetReadLayout method)
get_read_layout() (htsinfer.htsinfer.HtsInfer method)
get_read_orientation() (htsinfer.htsinfer.HtsInfer method)
get_source() (htsinfer.get_library_source.GetLibSource method)
get_source_expression() (htsinfer.get_library_source.GetLibSource static method)
get_source_name() (htsinfer.get_library_source.GetLibSource static method)
get_star_chr_bin_bits() (htsinfer.mapping.Mapping static method)
get_star_index_string_size() (htsinfer.mapping.Mapping static method)
GetAdapter3 (class in htsinfer.get_read_layout)
GetFastqType (class in htsinfer.get_library_type)
GetLibSource (class in htsinfer.get_library_source)
GetLibStats (class in htsinfer.get_library_stats)
GetLibType (class in htsinfer.get_library_type)
GetLibType.AlignedSegment (class in htsinfer.get_library_type)
GetOrientation (class in htsinfer.get_read_orientation)
GetReadLayout (class in htsinfer.get_read_layout)
H
htsinfer
module
HtsInfer (class in htsinfer.htsinfer)
htsinfer.cli
module
htsinfer.exceptions
module
htsinfer.get_library_source
module
htsinfer.get_library_stats
module
htsinfer.get_library_type
module
htsinfer.get_read_layout
module
htsinfer.get_read_orientation
module
htsinfer.htsinfer
module
htsinfer.mapping
module
htsinfer.models
module
htsinfer.subset_fastq
module
htsinfer.utils
module
I
InconsistentFastqIdentifiers
INFO (htsinfer.models.LogLevels attribute)
inward_stranded_forward (htsinfer.models.StatesOrientationRelationship attribute)
,
[1]
inward_stranded_reverse (htsinfer.models.StatesOrientationRelationship attribute)
,
[1]
inward_unstranded (htsinfer.models.StatesOrientationRelationship attribute)
,
[1]
K
KallistoProblem
KEEP_ALL (htsinfer.models.CleanupRegimes attribute)
KEEP_NONE (htsinfer.models.CleanupRegimes attribute)
KEEP_RESULTS (htsinfer.models.CleanupRegimes attribute)
L
Layout (class in htsinfer.models)
lib_source_min_freq_ratio (htsinfer.models.Args attribute)
,
[1]
lib_source_min_match_pct (htsinfer.models.Args attribute)
,
[1]
lib_type_mates_cutoff (htsinfer.models.Args attribute)
,
[1]
lib_type_max_distance (htsinfer.models.Args attribute)
,
[1]
library_source (htsinfer.get_read_orientation.GetOrientation attribute)
(htsinfer.models.Results attribute)
library_stats (htsinfer.models.Results attribute)
library_type (htsinfer.get_read_orientation.GetOrientation attribute)
(htsinfer.models.Results attribute)
LogLevels (class in htsinfer.models)
M
main() (in module htsinfer.cli)
Mapping (class in htsinfer.mapping)
max (htsinfer.models.ReadLength attribute)
,
[1]
mean (htsinfer.models.ReadLength attribute)
,
[1]
median (htsinfer.models.ReadLength attribute)
,
[1]
MetadataWarning
min (htsinfer.models.ReadLength attribute)
,
[1]
min_fraction (htsinfer.get_read_orientation.GetOrientation attribute)
min_freq_ratio (htsinfer.get_read_layout.GetAdapter3 attribute)
(htsinfer.get_read_layout.GetReadLayout attribute)
min_mapped_reads (htsinfer.get_read_orientation.GetOrientation attribute)
min_match_pct (htsinfer.get_read_layout.GetAdapter3 attribute)
(htsinfer.get_read_layout.GetReadLayout attribute)
mixed_mates (htsinfer.models.StatesType attribute)
,
[1]
mode (htsinfer.models.ReadLength attribute)
,
[1]
model_computed_fields (htsinfer.models.Args attribute)
(htsinfer.models.Config attribute)
(htsinfer.models.Layout attribute)
(htsinfer.models.ReadLength attribute)
(htsinfer.models.Results attribute)
(htsinfer.models.ResultsLayout attribute)
(htsinfer.models.ResultsOrientation attribute)
(htsinfer.models.ResultsSource attribute)
(htsinfer.models.ResultsStats attribute)
(htsinfer.models.ResultsType attribute)
(htsinfer.models.Source attribute)
(htsinfer.models.Stats attribute)
model_config (htsinfer.models.Args attribute)
(htsinfer.models.Config attribute)
(htsinfer.models.Layout attribute)
(htsinfer.models.ReadLength attribute)
(htsinfer.models.Results attribute)
(htsinfer.models.ResultsLayout attribute)
(htsinfer.models.ResultsOrientation attribute)
(htsinfer.models.ResultsSource attribute)
(htsinfer.models.ResultsStats attribute)
(htsinfer.models.ResultsType attribute)
(htsinfer.models.Source attribute)
(htsinfer.models.Stats attribute)
model_fields (htsinfer.models.Args attribute)
(htsinfer.models.Config attribute)
(htsinfer.models.Layout attribute)
(htsinfer.models.ReadLength attribute)
(htsinfer.models.Results attribute)
(htsinfer.models.ResultsLayout attribute)
(htsinfer.models.ResultsOrientation attribute)
(htsinfer.models.ResultsSource attribute)
(htsinfer.models.ResultsStats attribute)
(htsinfer.models.ResultsType attribute)
(htsinfer.models.Source attribute)
(htsinfer.models.Stats attribute)
module
htsinfer
htsinfer.cli
htsinfer.exceptions
htsinfer.get_library_source
htsinfer.get_library_stats
htsinfer.get_library_type
htsinfer.get_read_layout
htsinfer.get_read_orientation
htsinfer.htsinfer
htsinfer.mapping
htsinfer.models
htsinfer.subset_fastq
htsinfer.utils
N
n_processed (htsinfer.subset_fastq.SubsetFastq attribute)
not_available (htsinfer.models.StatesOrientation attribute)
,
[1]
(htsinfer.models.StatesOrientationRelationship attribute)
,
[1]
(htsinfer.models.StatesType attribute)
,
[1]
(htsinfer.models.StatesTypeRelationship attribute)
,
[1]
not_mates (htsinfer.models.StatesTypeRelationship attribute)
,
[1]
O
OKAY (htsinfer.models.RunStates attribute)
out_dir (htsinfer.get_read_layout.GetAdapter3 attribute)
(htsinfer.get_read_layout.GetReadLayout attribute)
(htsinfer.models.Args attribute)
,
[1]
(htsinfer.subset_fastq.SubsetFastq attribute)
out_path (htsinfer.subset_fastq.SubsetFastq attribute)
P
parse_args() (in module htsinfer.cli)
path (htsinfer.get_library_type.GetFastqType attribute)
(htsinfer.get_read_layout.GetAdapter3 attribute)
(htsinfer.subset_fastq.SubsetFastq attribute)
path_1 (htsinfer.get_read_layout.GetReadLayout attribute)
(htsinfer.mapping.Mapping attribute)
(htsinfer.models.Args attribute)
,
[1]
path_1_processed (htsinfer.models.Args attribute)
,
[1]
path_2 (htsinfer.get_read_layout.GetReadLayout attribute)
(htsinfer.mapping.Mapping attribute)
(htsinfer.models.Args attribute)
,
[1]
path_2_processed (htsinfer.models.Args attribute)
,
[1]
paths (htsinfer.get_library_stats.GetLibStats attribute)
(htsinfer.get_read_orientation.GetOrientation attribute)
polyA_frac (htsinfer.models.Layout attribute)
,
[1]
prepare_env() (htsinfer.htsinfer.HtsInfer method)
prepare_star_alignment_commands() (htsinfer.mapping.Mapping method)
print() (htsinfer.htsinfer.HtsInfer method)
process() (htsinfer.subset_fastq.SubsetFastq method)
process_alignments() (htsinfer.get_read_orientation.GetOrientation method)
process_inputs() (htsinfer.htsinfer.HtsInfer method)
process_paired() (htsinfer.get_read_orientation.GetOrientation method)
process_single() (htsinfer.get_read_orientation.GetOrientation method)
R
read_layout (htsinfer.models.Results attribute)
read_layout_adapter_file (htsinfer.models.Args attribute)
,
[1]
read_layout_min_freq_ratio (htsinfer.models.Args attribute)
,
[1]
read_layout_min_match_pct (htsinfer.models.Args attribute)
,
[1]
read_length (htsinfer.models.Stats attribute)
,
[1]
read_orientation (htsinfer.models.Results attribute)
read_orientation_min_fraction (htsinfer.models.Args attribute)
,
[1]
read_orientation_min_mapped_reads (htsinfer.models.Args attribute)
,
[1]
ReadLength (class in htsinfer.models)
records (htsinfer.models.Args attribute)
,
[1]
(htsinfer.subset_fastq.SubsetFastq attribute)
relationship (htsinfer.models.ResultsOrientation attribute)
(htsinfer.models.ResultsType attribute)
,
[1]
result (htsinfer.get_library_type.GetFastqType attribute)
(htsinfer.get_read_layout.GetAdapter3 attribute)
Results (class in htsinfer.models)
results (htsinfer.get_read_layout.GetReadLayout attribute)
(htsinfer.models.Args attribute)
(htsinfer.models.Config attribute)
,
[1]
ResultsLayout (class in htsinfer.models)
ResultsOrientation (class in htsinfer.models)
ResultsSource (class in htsinfer.models)
ResultsStats (class in htsinfer.models)
ResultsType (class in htsinfer.models)
run_id (htsinfer.htsinfer.HtsInfer attribute)
(htsinfer.models.Args attribute)
run_kallisto_quantification() (htsinfer.get_library_source.GetLibSource method)
RunStates (class in htsinfer.models)
S
SamFileProblem
second_mate (htsinfer.models.StatesType attribute)
,
[1]
second_mate_assumed (htsinfer.models.StatesType attribute)
seq_id_format (htsinfer.get_library_type.GetFastqType attribute)
seq_ids (htsinfer.get_library_type.GetFastqType attribute)
SeqIdFormats (class in htsinfer.models)
setup_logging() (in module htsinfer.cli)
short_name (htsinfer.models.Source attribute)
,
[1]
single (htsinfer.models.StatesType attribute)
,
[1]
Source (class in htsinfer.models)
split_mates (htsinfer.models.StatesTypeRelationship attribute)
,
[1]
StarProblem
state (htsinfer.htsinfer.HtsInfer attribute)
(htsinfer.models.Args attribute)
StatesOrientation (class in htsinfer.models)
StatesOrientationRelationship (class in htsinfer.models)
StatesType (class in htsinfer.models)
StatesTypeRelationship (class in htsinfer.models)
Stats (class in htsinfer.models)
stranded_forward (htsinfer.models.StatesOrientation attribute)
,
[1]
stranded_reverse (htsinfer.models.StatesOrientation attribute)
,
[1]
subset_transcripts_by_organism() (htsinfer.mapping.Mapping method)
SubsetFastq (class in htsinfer.subset_fastq)
sum_dicts() (htsinfer.get_read_orientation.GetOrientation static method)
T
t_file_processed (htsinfer.models.Args attribute)
,
[1]
tax_id (htsinfer.models.Args attribute)
taxon_id (htsinfer.models.Source attribute)
,
[1]
threads (htsinfer.models.Args attribute)
,
[1]
threads_star (htsinfer.get_read_orientation.GetOrientation attribute)
tmp_dir (htsinfer.get_library_stats.GetLibStats attribute)
(htsinfer.get_read_orientation.GetOrientation attribute)
(htsinfer.models.Args attribute)
,
[1]
transcripts_file (htsinfer.get_read_orientation.GetOrientation attribute)
(htsinfer.models.Args attribute)
,
[1]
TranscriptsFastaProblem
trie (htsinfer.get_read_layout.GetAdapter3 attribute)
U
UnknownFastqIdentifier
unstranded (htsinfer.models.StatesOrientation attribute)
,
[1]
UnsupportedSampleSourceException
V
validate_top_score() (in module htsinfer.utils)
W
WARN (htsinfer.models.LogLevels attribute)
WARNING (htsinfer.models.LogLevels attribute)
(htsinfer.models.RunStates attribute)
WorkEnvProblem
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