reconstruction.ecoli.scripts.fold_changes.calculate_fc

Aggregate data from Javi’s repo to compare to fold_changes.tsv included in wcm.

reconstruction.ecoli.scripts.fold_changes.calculate_fc.compare_data(data1, data2, desc, verbose=True)

Compares regulation from source data to wcm data.

Parameters:

• data1 (dict[str, dict[str, dict[str, float]]]) – mean and standard deviation for each regulatory pair

• data2 (dict[str, dict[str, dict[str, float]]]) – mean and standard deviation for each regulatory pair

• desc (str) – description for comparison

• verbose (bool) – if True, prints additional regulation information

Notes

dictionary structure for both inputs:

{TF gene name: {regulated gene: {‘mean’: mean, ‘std’: std}}}

reconstruction.ecoli.scripts.fold_changes.calculate_fc.load_file(filename)

Load a tsv file.

Parameters:

filename (str)

Return type:

list[list[str]]

reconstruction.ecoli.scripts.fold_changes.calculate_fc.load_shifts()

Load TF regulation information for each shift.

Returns:

gene regulation direction for each condition

1 for active TF in condition1 vs condition2 -1 for active TF in condition2 vs condition1 {(condition1, condition2): {TF1: 1, TF2: -1, …}}

Return type:

shifts

reconstruction.ecoli.scripts.fold_changes.calculate_fc.load_src(attempt_match)

Loads and extracts gene regulation data from the source data.

Parameters:

attempt_match (bool) – if True, handles data in way that was most likely the original processing, otherwise uses expected directionality

Returns:

mean and standard deviation for each regulatory pair

{TF gene name: {regulated gene: {‘mean’: mean, ‘std’: std}}}

Return type:

data

reconstruction.ecoli.scripts.fold_changes.calculate_fc.load_wcm(attempt_match)

Loads and extracts gene regulation data from the whole-cell model.

Parameters:

attempt_match (bool) – if True, handles data in way that was most likely the original processing, otherwise uses expected directionality

Returns:

mean and standard deviation for each regulatory pair

{TF gene name: {regulated gene: {‘mean’: mean, ‘std’: std}}}

Return type:

data

reconstruction.ecoli.scripts.fold_changes.calculate_fc.parse_args()

Parses arguments from the command line.

Returns:

values of variables parsed from the command line

Return type:

Namespace

reconstruction.ecoli.scripts.fold_changes.calculate_fc.replace_uncertain_entries(data)

Replaces entries that were marked as uncertain in fold changes (Regulation_direct 3 or 4) if the mean fold change is the opposite sign when correcting for the regulation direction.

Parameters:

data (dict[str, dict[str, dict[str, float]]]) – mean and standard deviation for each regulatory pair