psctb.modeltools package¶

Submodules¶

psctb.modeltools._paths module¶

psctb.modeltools._paths.get_file_path(working_dir, internal_filename, fmt, fixed=None, file_name=None, write_suffix=True)[source]¶

An heuristic for determining the correct file name.

This function determines the file name according to the information supplied by the user and the internals of a specific class.

Parameters

working_dirstr

The working dir of the specific class (where files are saved if no file name is supplied)

internal_filenamestr

The default base name (sans numbered suffix) of files when no other details are provided.

fmtstr

The format (extension) that the file should be saved in. This is used both in determining file name if no file name is provided as well as when a file name without extension is provided.

fixedstr, Optional (DefaultNone)

In the case that a metabolite is fixed, files will be saved in a subdirectory of the working directory that corresponds to the fixed metabolite.

file_namestr, Optional (DefaultNone): If a file name is supplied it overwrites all other options except fmt in the case where no extension is supplied.

Returns

——-

str

The final file name

psctb.modeltools._paths.get_fmt(file_name)[source]¶

Gets the extension (fmt) from a file name.

Parameters

file_namestr: The file to get an extension from

Returns

str: The extension string

psctb.modeltools._paths.get_model_name(mod)[source]¶

Returns the file name of a pysces model object sans the file extension.

Parameters

modPysMod: Model of interest.

Returns

str: File name of a mod sans extension.

psctb.modeltools._paths.make_path(mod, analysis_method, subdirs=[])[source]¶

Creates paths based on model name and analysis type.

This function is used to create directories (in the case where they don’t already exist) to write analysis results to and return the path name. Subdirectories can also be created.

/path/to/Pysces/model_name/analysis_method/subdir1/subdir2/

Parameters

modPysMod: The model being analysed.
analysis_methodstr: The name of the tool being used to analyse the model.
subdirslist of str: An optional list of subdirectories where each additional entry in the list will create a subdirectory in the previous directories.

Returns

str: The directory string

Examples

>>> print make_path(mod, 'analysis_method', subdirs = ['subdir1', subdir2])
'/path/to/Pysces/model_name/analysis_method/subdir1/subdir2/'

psctb.modeltools._paths.next_suffix(directory, base_name, ext=None)[source]¶

Returns the number of the next suffix to be appended to a base file name when saving a file.

This function checks a directory for files containing base_name and returns a number that is equal to the suffix of a file named base_name with the largest suffix plus one.

Parameters

directorystr: The directory to inspect for files.
base_namestr: The base name (sans suffix) to check for.

Returns

int: The next suffix to write

psctb.modeltools._pscmanipulate module¶

psctb.modeltools._pscmanipulate.augment_fix_sting(OrigFix, fix)[source]¶

Adds a species to a psc file header.

Parameters

OrigFixstr: A psc file header
fixstr: Additional species to add to psc file header.

Returns

str: A new psc file header that contains the contents of the original together with the new fixed species.

psctb.modeltools._pscmanipulate.fix_metabolite(mod, fix, model_name=None)[source]¶

Fix a metabolite in a model and return a new model with the fixed metabolite.

Parameters

modPysMod: The original model.
fixstr: The metabolite to fix.
model_namestr, optional (Defaultnone): The file name to use when saving the model (in psc/orca). If None it defaults to original_model_name_fix.

Returns

PysMod: A new model instance with an additional fixed species.

psctb.modeltools._pscmanipulate.fix_metabolite_ss(mod, fix, model_name=None)[source]¶

Fix a metabolite at its steady state in a model and return a new model with the fixed metabolite.

Parameters

modPysMod: The original model.
fixstr: The metabolite to fix.
model_namestr, optional (Defaultnone): The file name to use when saving the model (in psc/orca). If None it defaults to original_model_name_fix.

Returns

PysMod: A new model instance with an additional fixed species.

psctb.modeltools package¶

Submodules¶

psctb.modeltools._paths module¶

psctb.modeltools._pscmanipulate module¶

Module contents¶