hybkit.settings
This module contains settings information for hybkit classes and methods.
- hybkit.settings.HYB_SUFFIXES = ['.hyb', '.Hyb', '.HYB']
Allowed suffixes for "Hyb" files.
- hybkit.settings.VIENNA_SUFFIXES = ['.vienna', '.Vienna', '.VIENNA']
Allowed suffixes for "Vienna" files.
- hybkit.settings.CT_SUFFIXES = ['.ct', '.Ct', '.CT']
Allowed suffixes for "Connection-Table" files.
- hybkit.settings.FOLD_SUFFIXES = ['.vienna', '.Vienna', '.VIENNA', '.ct', '.Ct', '.CT']
Allowed suffixes for "Vienna" and "Connection-Table" files.
- hybkit.settings.MIRNA_TYPES = ['miRNA', 'microRNA']
Default miRNA types for use in
mirna_analysis().
- hybkit.settings.HybRecord_settings_info
Information for settings of
HybRecordclass. Copied intoHybRecord_settingsfor use at runtime.
hybkit.settings.HybRecord_settings_info = {
'allow_undefined_flags': {'Argp-Flag': None,
'Argp-Opts': {'const': True, 'nargs': '?'},
'Argp-Type': 'custom_bool_from_str',
'Def-Val': False,
'Desc.': 'Allow use of flags not defined in the '
'hybkit-specification order when reading and '
'writing hyb records. As the preferred '
'alternative to using this setting, the '
'--custom_flags argument can be be used to '
'supply custom allowed flags.'},
'allow_unknown_seg_types': {'Argp-Flag': None,
'Argp-Opts': {'const': True, 'nargs': '?'},
'Argp-Type': 'custom_bool_from_str',
'Def-Val': False,
'Desc.': 'Allow unknown segment types when assigning '
'segment types.'},
'custom_flags': {'Argp-Flag': None,
'Argp-Opts': {'nargs': '+'},
'Argp-Type': 'str',
'Def-Val': [],
'Desc.': 'Custom flags to allow in addition to those specified in '
'the hybkit specification.'},
'hyb_placeholder': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'str',
'Def-Val': '.',
'Desc.': 'placeholder character/string for missing data in hyb '
'files.'},
'mirna_types': {'Argp-Flag': None,
'Argp-Opts': {'nargs': '+'},
'Argp-Type': 'str',
'Def-Val': ['miRNA', 'microRNA'],
'Desc.': '"seg_type" fields identifying a miRNA'},
'reorder_flags': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'custom_bool_from_str',
'Def-Val': True,
'Desc.': 'Re-order flags to the hybkit-specification order when '
'writing hyb records.'}
}
- hybkit.settings.HybFile_settings_info
Information for settings of
HybFileclass. Copied intoHybFile_settingsfor use at runtime.
hybkit.settings.HybFile_settings_info = {
'hybformat_id': {'Argp-Flag': None,
'Argp-Opts': {'const': True, 'nargs': '?'},
'Argp-Type': 'custom_bool_from_str',
'Def-Val': False,
'Desc.': 'The Hyb Software Package places further information in '
'the "id" field of the hybrid record that can be used to '
'infer the number of contained read counts. When set to '
'True, the identifiers will be parsed as: '
'"<read_id>_<read_count>"'},
'hybformat_ref': {'Argp-Flag': None,
'Argp-Opts': {'const': True, 'nargs': '?'},
'Argp-Type': 'custom_bool_from_str',
'Def-Val': False,
'Desc.': 'The Hyb Software Package uses a reference database '
'with identifiers that contain sequence type and other '
'sequence information. When set to True, all hyb file '
'identifiers will be parsed as: '
'"<gene_id>_<transcript_id>_<gene_name>_<seg_type>"'}
}
- hybkit.settings.FoldRecord_settings_info
Information for settings of
FoldRecordclass. Copied intoFoldRecord_settingsfor use at runtime.
hybkit.settings.FoldRecord_settings_info = {
'allowed_mismatches': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'int',
'Def-Val': 0,
'Desc.': 'For DynamicFoldRecords, allowed number of '
'mismatches with a HybRecord.'},
'error_mode': {'Argp-Flag': None,
'Argp-Opts': {'choices': ['raise', 'warn_return', 'return']},
'Argp-Type': 'str',
'Def-Val': 'raise',
'Desc.': 'Mode for handling errors during reading of HybFiles '
"(overridden by HybFoldIter.settings['iter_error_mode'] "
'when using HybFoldIter). Options: "raise": Raise an error '
'when encountered and exit program ; "warn_return": Print '
'a warning and return the error_value ; "return": Return '
'the error value with no program output. record is '
'encountered.'},
'fold_placeholder': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'str',
'Def-Val': '.',
'Desc.': 'Placeholder character/string for missing data for '
'reading/writing fold records.'},
'seq_type': {'Argp-Flag': '-y',
'Argp-Opts': {'choices': ['static', 'dynamic']},
'Argp-Type': 'str',
'Def-Val': 'static',
'Desc.': 'Type of fold record object to use. Options: "static": '
'FoldRecord, requires an exact sequence match to be paired '
'with a HybRecord; "dynamic": DynamicFoldRecord, requires a '
'sequence match to the "dynamic" annotated regions of a '
'HybRecord, and may be shorter/longer than the original '
'sequence.'}
}
- hybkit.settings.FoldFile_settings_info
Information for settings of
FoldFileclass. Copied intoFoldFile_settingsfor use at runtime.
hybkit.settings.FoldFile_settings_info = {
}
- hybkit.settings.HybFoldIter_settings_info
Information for settings of
HybFoldIterclass. Copied intoHybFoldIter_settingsfor use at runtime.
hybkit.settings.HybFoldIter_settings_info = {
'error_checks': {'Argp-Flag': None,
'Argp-Opts': {'choices': ['hybrecord_indel',
'foldrecord_nofold',
'max_mismatch',
'energy_mismatch']},
'Argp-Type': 'str',
'Def-Val': ['hybrecord_indel',
'foldrecord_nofold',
'max_mismatch',
'energy_mismatch'],
'Desc.': 'Error checks for simultaneous HybFile and FoldFile '
'parsing. Options: "hybrecord_indel": Error for '
'HybRecord objects where one/both sequences have '
'insertions/deletions in alignment, which prevents '
'matching of sequences; "foldrecord_nofold": Error when '
'failure in reading a fold_record object; '
'"max_mismatch": Error when mismatch between hybrecord '
'and foldrecord sequences is greater than FoldRecord '
'"allowed_mismatches" setting; "energy_mismatch": Error '
'when a mismatch exists between HybRecord and FoldRecord '
'energy values.'},
'iter_error_mode': {'Argp-Flag': None,
'Argp-Opts': {'choices': ['raise',
'warn_return',
'warn_skip',
'skip',
'return']},
'Argp-Type': 'str',
'Def-Val': 'warn_skip',
'Desc.': 'Mode for handling errors found during error checks. '
'Overrides HybRecord "error_mode" setting when using '
'HybFoldIter. Options: "raise": Raise an error when '
'encountered; "warn_return": Print a warning and '
'return the value; "warn_skip": Print a warning and '
'continue to the next iteration; "skip": Continue to '
'the next iteration without any output; "return": '
'return the value without any error output;'},
'max_sequential_skips': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'int',
'Def-Val': 100,
'Desc.': 'Maximum number of record(-pairs) to skip in a '
'row. Limited as several sequential skips '
'usually indicates an issue with record '
'formatting or a desynchronization between '
'files.'}
}
- hybkit.settings.Analysis_settings_info
Information for settings of
Analysisclass. Copied intoAnalysis_settingsfor use at runtime.
hybkit.settings.Analysis_settings_info = {
'out_delim': {'Argp-Flag': None,
'Argp-Opts': {},
'Argp-Type': 'str',
'Def-Val': ',',
'Desc.': 'Delimiter-string to place between fields in analysis '
'output.'},
'quant_mode': {'Argp-Flag': None,
'Argp-Opts': {'choices': ['single', 'reads', 'records']},
'Argp-Type': 'str',
'Def-Val': 'single',
'Desc.': 'Method for counting records. Options: "single": Count '
'each record as a single entry; "reads": Use the number of '
'reads per hyb record as the count (may contain PCR '
'duplicates); "records": Count the number of records '
'represented by each hyb record entry (1 for "unmerged" '
'records, >= 1 for "merged" records)'}
}
- hybkit.settings.HybRecord_settings = {'allow_undefined_flags': False, 'allow_unknown_seg_types': False, 'custom_flags': [], 'hyb_placeholder': '.', 'mirna_types': ['miRNA', 'microRNA'], 'reorder_flags': True}
Settings for
HybRecord, created fromHybRecord_settings_info
- hybkit.settings.HybFile_settings = {'hybformat_id': False, 'hybformat_ref': False}
Settings for
HybFile, created fromHybFile_settings_info
- hybkit.settings.FoldRecord_settings = {'allowed_mismatches': 0, 'error_mode': 'raise', 'fold_placeholder': '.', 'seq_type': 'static'}
Settings for
FoldRecord, created fromFoldRecord_settings_info
- hybkit.settings.FoldFile_settings = {}
Settings for
FoldFile, created fromFoldFile_settings_info
- hybkit.settings.HybFoldIter_settings = {'error_checks': ['hybrecord_indel', 'foldrecord_nofold', 'max_mismatch', 'energy_mismatch'], 'iter_error_mode': 'warn_skip', 'max_sequential_skips': 100}
Settings for
HybFoldIter, created fromHybFoldIter_settings_info
- hybkit.settings.Analysis_settings = {'out_delim': ',', 'quant_mode': 'single'}
Settings for
BaseAnalysis, created fromAnalysis_settings_info