hybkit
stable
Documentation Contents:
hybkit
hybkit Hyb File Specification
hybkit API
hybkit Toolkit
Example Analyses
About
References
hybkit
Index
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Index
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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K
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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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V
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W
A
add_hyb_record() (hybkit.analysis.Analysis method)
add_hyb_records() (hybkit.analysis.Analysis method)
ALL_FLAGS (hybkit.HybRecord attribute)
Analysis (class in hybkit.analysis)
analysis_options (hybkit.analysis.Analysis attribute)
Analysis_settings (in module hybkit.settings)
Analysis_settings_info (in module hybkit.settings)
B
BAR_DEFAULTS (in module hybkit.plot)
BAR_INT_DEFAULTS (in module hybkit.plot)
C
check_set_method() (hybkit.type_finder.TypeFinder class method)
close() (hybkit.CtFile method)
(hybkit.HybFile method)
(hybkit.ViennaFile method)
COLOR_DICT (in module hybkit.plot)
COLOR_LIST (in module hybkit.plot)
count_hyb_record_mismatches() (hybkit.FoldRecord method)
ct_exists() (in module hybkit.util)
CT_SUFFIXES (in module hybkit.settings)
CtFile (class in hybkit)
D
default_method (hybkit.type_finder.TypeFinder attribute)
dir_exists() (in module hybkit.util)
dynamic_count_hyb_record_mismatches() (hybkit.FoldRecord method)
E
ENERGY_DEFAULTS (in module hybkit.plot)
ENERGY_HIST_RC_PARAMS (in module hybkit.plot)
energy_histogram() (in module hybkit.plot)
ensure_matches_hyb_record() (hybkit.FoldRecord method)
eval_mirna() (hybkit.HybRecord method)
eval_types() (hybkit.HybRecord method)
F
file_exists() (in module hybkit.util)
find() (hybkit.type_finder.TypeFinder class method)
find_with_params (hybkit.type_finder.TypeFinder attribute)
fold_exists() (in module hybkit.util)
fold_match_counts_histogram() (in module hybkit.plot)
FOLD_MATCH_HIST_RC_PARAMS (in module hybkit.plot)
fold_mirna_nt_counts_histogram() (in module hybkit.plot)
FOLD_NT_COUNTS_HIST_RC_PARAMS (in module hybkit.plot)
FOLD_SUFFIXES (in module hybkit.settings)
FoldFile_settings (in module hybkit.settings)
FoldFile_settings_info (in module hybkit.settings)
FoldRecord (class in hybkit)
FoldRecord_settings (in module hybkit.settings)
FoldRecord_settings_info (in module hybkit.settings)
from_ct_lines() (hybkit.FoldRecord class method)
from_ct_string() (hybkit.FoldRecord class method)
from_fasta_records() (hybkit.HybRecord class method)
from_line() (hybkit.HybRecord class method)
from_vienna_lines() (hybkit.FoldRecord class method)
from_vienna_string() (hybkit.FoldRecord class method)
G
GEN_PROPS (hybkit.HybRecord attribute)
get_all_results() (hybkit.analysis.Analysis method)
get_analysis_delim_str() (hybkit.analysis.Analysis method)
get_analysis_results() (hybkit.analysis.Analysis method)
get_argparse_doc() (in module hybkit.util)
get_mirna_props() (hybkit.HybRecord method)
get_read_count() (hybkit.HybRecord method)
get_record_count() (hybkit.HybRecord method)
get_seg1_type() (hybkit.HybRecord method)
get_seg2_type() (hybkit.HybRecord method)
get_seg_types() (hybkit.HybRecord method)
get_specific_result() (hybkit.analysis.Analysis method)
get_target_props() (hybkit.HybRecord method)
H
has_prop() (hybkit.HybRecord method)
HAS_PROPS (hybkit.HybRecord attribute)
hyb_analyze
module
hyb_check
module
hyb_eval
module
hyb_exists() (in module hybkit.util)
hyb_filter
module
HYB_SUFFIXES (in module hybkit.settings)
HybFile (class in hybkit)
HybFile_settings (in module hybkit.settings)
HybFile_settings_info (in module hybkit.settings)
HybFoldIter (class in hybkit)
HybFoldIter_settings (in module hybkit.settings)
HybFoldIter_settings_info (in module hybkit.settings)
hybkit
module
hybkit.analysis
module
hybkit.errors
module
hybkit.plot
module
hybkit.settings
module
hybkit.type_finder
module
hybkit.util
module
HybkitArgError
HybkitConstructorError
HybkitError
HybkitIterError
HybkitMiscError
HybRecord (class in hybkit)
HybRecord_settings (in module hybkit.settings)
HybRecord_settings_info (in module hybkit.settings)
HYBRID_COLUMNS (hybkit.HybRecord attribute)
I
is_set() (hybkit.HybRecord method)
K
key (hybkit.analysis.Analysis attribute)
M
make_id_map_params() (hybkit.type_finder.TypeFinder static method)
make_out_file_name() (in module hybkit.util)
make_string_match_params() (hybkit.type_finder.TypeFinder static method)
matches_hyb_record() (hybkit.FoldRecord method)
method_hybformat() (hybkit.type_finder.TypeFinder static method)
method_id_map() (hybkit.type_finder.TypeFinder static method)
method_is_set() (hybkit.type_finder.TypeFinder class method)
method_string_match() (hybkit.type_finder.TypeFinder static method)
methods (hybkit.type_finder.TypeFinder attribute)
mirna_detail() (hybkit.HybRecord method)
mirna_details() (hybkit.HybRecord method)
MIRNA_PROPS (hybkit.HybRecord attribute)
MIRNA_STR_PROPS (hybkit.HybRecord attribute)
MIRNA_TYPES (in module hybkit.settings)
module
hyb_analyze
hyb_check
hyb_eval
hyb_filter
hybkit
hybkit.analysis
hybkit.errors
hybkit.plot
hybkit.settings
hybkit.type_finder
hybkit.util
N
not_set() (hybkit.HybRecord method)
O
open() (hybkit.CtFile class method)
(hybkit.HybFile class method)
(hybkit.ViennaFile class method)
out_path_exists() (in module hybkit.util)
P
param_methods (hybkit.type_finder.TypeFinder attribute)
param_methods_needs_file (hybkit.type_finder.TypeFinder attribute)
params (hybkit.type_finder.TypeFinder attribute)
PIE_DEFAULTS (in module hybkit.plot)
plot_analysis_results() (hybkit.analysis.Analysis method)
print_report() (hybkit.HybFoldIter method)
prop() (hybkit.HybRecord method)
R
read_record() (hybkit.CtFile method)
(hybkit.HybFile method)
(hybkit.ViennaFile method)
read_records() (hybkit.CtFile method)
(hybkit.HybFile method)
(hybkit.ViennaFile method)
report() (hybkit.HybFoldIter method)
S
SEGMENT_COLUMNS (hybkit.HybRecord attribute)
set_custom_method() (hybkit.type_finder.TypeFinder class method)
set_flag() (hybkit.HybRecord method)
set_fold_record() (hybkit.HybRecord method)
set_method() (hybkit.type_finder.TypeFinder class method)
SET_PROPS (hybkit.HybRecord attribute)
set_setting() (in module hybkit.util)
set_settings_from_namespace() (in module hybkit.util)
settings (hybkit.analysis.Analysis attribute)
(hybkit.CtFile attribute)
(hybkit.FoldRecord attribute)
(hybkit.HybFile attribute)
(hybkit.HybFoldIter attribute)
(hybkit.HybRecord attribute)
(hybkit.ViennaFile attribute)
static_count_hyb_record_mismatches() (hybkit.FoldRecord method)
STR_PROPS (hybkit.HybRecord attribute)
T
target_count() (in module hybkit.plot)
TARGET_PIE_RC_PARAMS (in module hybkit.plot)
to_csv() (hybkit.HybRecord method)
to_csv_header() (hybkit.HybRecord class method)
to_fasta_record() (hybkit.HybRecord method)
to_fasta_str() (hybkit.HybRecord method)
to_fields() (hybkit.HybRecord method)
to_fields_header() (hybkit.HybRecord class method)
to_line() (hybkit.HybRecord method)
to_vienna_lines() (hybkit.FoldRecord method)
to_vienna_string() (hybkit.FoldRecord method)
type_count() (in module hybkit.plot)
type_count_dual() (in module hybkit.plot)
TYPE_PIE_DUAL_RC_PARAMS (in module hybkit.plot)
TYPE_PIE_SINGLE_RC_PARAMS (in module hybkit.plot)
TypeFinder (class in hybkit.type_finder)
(hybkit.HybRecord attribute)
V
validate_args() (in module hybkit.util)
validate_args_exit() (in module hybkit.util)
vienna_exists() (in module hybkit.util)
VIENNA_SUFFIXES (in module hybkit.settings)
ViennaFile (class in hybkit)
W
write() (hybkit.HybFile method)
write_analysis_delim_str() (hybkit.analysis.Analysis method)
write_analysis_results_special() (hybkit.analysis.Analysis method)
write_fh() (hybkit.CtFile method)
(hybkit.HybFile method)
(hybkit.ViennaFile method)
write_record (hybkit.CtFile attribute)
write_record() (hybkit.HybFile method)
(hybkit.ViennaFile method)
write_records (hybkit.CtFile attribute)
write_records() (hybkit.HybFile method)
(hybkit.ViennaFile method)
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