reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat

Extracts concentrations for metabolites from various raw data files.

Data in lempp2019.tsv was converted to a tsv from the file downloaded from Lempp et al. Systematic identification of metabolites controlling gene expression in E. coli. 2019. https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-019-12474-1/MediaObjects/41467_2019_12474_MOESM4_ESM.xlsx

Data in park2016.tsv was converted to a tsv from supplementary table 5 (manually removed some columns and rows) in the file downloaded from https://static-content.springer.com/esm/art%3A10.1038%2Fnchembio.2077/MediaObjects/41589_2016_BFnchembio2077_MOESM583_ESM.pdf

Data in kochanowski2017*.tsv was converted to a tsv from EV table 6-1 (absolute) and EV table 6-2 (relative) (manually removed some rows) from the file downloaded from https://www.embopress.org/action/downloadSupplement?doi=10.15252%2Fmsb.20167402&file=msb167402-sup-0007-TableEV6.xlsx

Data in sander2019.tsv is from Sander et al. Allosteric Feedback Inhibition Enables Robust Amino Acid Biosynthesis in E. coli by Enforcing Enzyme Overabundance. 2019 Table S7 (tab ‘Amino Acids’) from https://ars.els-cdn.com/content/image/1-s2.0-S2405471218304794-mmc2.xlsx

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.kegg_to_ecocyc(data)

Convert a dictionary with KEGG ID keys to a dictionary with EcoCyc ID keys.

Parameters:

data (dict[str, Any]) – dictionary to convert KEGG molecule IDs to EcoCyc IDs

Returns:

new dictionary with EcoCyc IDs

Return type:

new_data

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.kochanowski_concentrations()

Load absolute Kochanowski concentration data in the glucose condition.

Returns:

WCM ID to concentration (in M)

Return type:

met_conc

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.lempp_concentrations()

Load Lempp data for average metabolite concentrations at the first time point.

Returns:

EcoCyc molecule ID to concentration (in M)

Return type:

met_conc

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.load_kochanowski(filename)

Load Kochanowski data (absolute or relative).

Parameters:

filename (str) – path to file to load

Returns:

WCM ID to concentration (absolute or relative)

Return type:

met_conc

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.park_concentrations()

Load Park data for reported metabolite concentrations.

Returns:

EcoCyc molecule ID to concentration (in M)

Return type:

met_conc

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.sander_concentrations()

Load Sander data for amino acid concentrations.

Returns:

WCM ID to concentration (in M)

Return type:

met_conc

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.save_concentrations(conc, label)

Save EcoCyc ID concentrations to a file.

Parameters:

• conc (dict[str, float]) – ID to concentration (in M)

• label (str) – column and filename dataset label (author)

reconstruction.ecoli.scripts.metabolite_concentrations.convert_to_flat.save_kochanowski_relative_changes()

Convert relative Kochanowski concentration data to wcm IDs for all conditions.