petab.core¶
PEtab core functions (or functions that don’t fit anywhere else)
Functions
concat_tables (tables, …) |
Concatenate DataFrames provided as DataFrames or filenames, and a parser |
create_combine_archive (yaml_file, filename, …) |
Create COMBINE archive (http://co.mbine.org/documents/archive) based on PEtab YAML file. |
flatten_timepoint_specific_output_overrides (…) |
Flatten timepoint-specific output parameter overrides. |
get_notnull_columns (df, candidates) |
Return list of df -columns in candidates which are not all null/nan. |
get_observable_id (parameter_id) |
Get PEtab observable ID from PEtab-style sigma or observable AssignmentRule-target parameter_id . |
get_simulation_df (simulation_file) |
Read PEtab simulation table |
get_visualization_df (visualization_file) |
Read PEtab visualization table |
is_empty (val) |
Check if the value val, e.g. |
to_float_if_float (x) |
Return input as float if possible, otherwise return as is |
write_simulation_df (df, filename) |
Write PEtab simulation table |
write_visualization_df (df, filename) |
Write PEtab visualization table |
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petab.core.
concat_tables
(tables: Union[str, pandas.core.frame.DataFrame, Iterable[Union[pandas.core.frame.DataFrame, str]]], file_parser: Optional[Callable] = None) → pandas.core.frame.DataFrame¶ Concatenate DataFrames provided as DataFrames or filenames, and a parser
Parameters: - tables – Iterable of tables to join, as DataFrame or filename.
- file_parser – Function used to read the table in case filenames are provided, accepting a filename as only argument.
Returns: The concatenated DataFrames
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petab.core.
create_combine_archive
(yaml_file: str, filename: str, family_name: Optional[str] = None, given_name: Optional[str] = None, email: Optional[str] = None, organization: Optional[str] = None) → None¶ Create COMBINE archive (http://co.mbine.org/documents/archive) based on PEtab YAML file.
Parameters: - yaml_file – Path to PEtab YAML file
- family_name – Family name of archive creator
- given_name – Given name of archive creator
- email – E-mail address of archive creator
- organization – Organization of archive creator
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petab.core.
flatten_timepoint_specific_output_overrides
(petab_problem: petab.problem.Problem) → None¶ Flatten timepoint-specific output parameter overrides.
If the PEtab problem definition has timepoint-specific observableParameters or noiseParameters for the same observable, replace those by replicating the respective observable.
This is a helper function for some tools which may not support such timepoint-specific mappings. The observable table and measurement table are modified in place.
Parameters: petab_problem – PEtab problem to work on
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petab.core.
get_notnull_columns
(df: pandas.core.frame.DataFrame, candidates: Iterable[T_co])¶ Return list of
df
-columns incandidates
which are not all null/nan.The output can e.g. be used as input for
pandas.DataFrame.groupby
.Parameters: - df – Dataframe
- candidates – Columns of
df
to consider
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petab.core.
get_observable_id
(parameter_id: str) → str¶ Get PEtab observable ID from PEtab-style sigma or observable AssignmentRule-target
parameter_id
.e.g. for ‘observable_obs1’ -> ‘obs1’, for ‘sigma_obs1’ -> ‘obs1’
Parameters: parameter_id – Some parameter ID Returns: Observable ID
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petab.core.
get_simulation_df
(simulation_file: str) → pandas.core.frame.DataFrame¶ Read PEtab simulation table
Parameters: simulation_file – URL or filename of PEtab simulation table Returns: Simulation DataFrame
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petab.core.
get_visualization_df
(visualization_file: str) → pandas.core.frame.DataFrame¶ Read PEtab visualization table
Parameters: visualization_file – URL or filename of PEtab visualization table Returns: Visualization DataFrame
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petab.core.
is_empty
(val) → bool¶ Check if the value val, e.g. a table entry, is empty.
Parameters: val – The value to check. Returns: Whether the field is to be considered empty. Return type: empty
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petab.core.
to_float_if_float
(x: Any) → Any¶ Return input as float if possible, otherwise return as is
Parameters: x – Anything Returns: x
as float if possible, otherwisex
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petab.core.
write_simulation_df
(df: pandas.core.frame.DataFrame, filename: str) → None¶ Write PEtab simulation table
Parameters: - df – PEtab simulation table
- filename – Destination file name
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petab.core.
write_visualization_df
(df: pandas.core.frame.DataFrame, filename: str) → None¶ Write PEtab visualization table
Parameters: - df – PEtab visualization table
- filename – Destination file name