reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat

Extracts half-lives of RNAs from Supplementary Table S4 of Chen et al., “Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli” (2014) and Supporting Table 5 of Bernstein et al., “Global analysis of mRNA decay and abundance in Escherichi coli at single gene resoluation using two-color fluorescent DNA microarrays” (2002). Optionally generates a comparison plot for degradation rates reported for the same gene from these two sources.

reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.build_half_life_table(chen_half_lives, bernstein_half_lives, all_gene_ids)

Builds the RNA half-life flat file that is used as raw_data for the simulation using the data from the two papers. If data for a gene exists in both papers, we use data from Chen et al. assuming that their methodology is more accurate. In the output file monocistronic RNAs (represented by their corresponding gene IDs) are listed first, followed by polycistronic RNAs.

Parameters:

• chen_half_lives (Dict[str, float]) –

• bernstein_half_lives (Dict[str, float]) –

• all_gene_ids (Set[str]) –

Return type:

None

reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.compare_half_lives(chen_half_lives, bernstein_half_lives)

Generates a scatter plot that compares the half-lives of RNAs reported in both Chen et al. and Bernstein et al.

Parameters:

• chen_half_lives (Dict[str, float]) –

• bernstein_half_lives (Dict[str, float]) –

Return type:

None

reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.get_bernstein_half_lives(symbols_to_ids)

Reads RNA half lives reported by Bernstein et al., and stores them in a dictionary. Any gene listed that does not exist in the model are skipped. Bernstein et al. only reports half-lives of monocistronic RNAs.

Parameters:

• symbols_to_ids (Dict[str, str]) – Dictionary that maps gene/transcription unit symbols

• model. (to gene/transcription unit IDs used by the) –

Returns:

Dictionary that maps gene IDs to their RNA half lives (in minutes) reported by Bernstein et al.

Return type:

id_to_half_life

reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.get_chen_half_lives(symbols_to_ids)

Reads RNA half lives reported by Chen et al., and stores them in a dictionary. Any gene/transcription unit listed that does not exist in the model are skipped.

Parameters:

• symbols_to_ids (Dict[str, str]) – Dictionary that maps gene/transcription unit symbols

• model. (to gene/transcription unit IDs used by the) –

Returns:

Dictionary that maps gene/transcription unit IDs to their half lives (in minutes) reported by Chen et al.

Return type:

id_to_half_life

reconstruction.ecoli.scripts.rna_half_lives.convert_to_flat.get_symbols_to_ids()

Builds a mapping from gene/transcription unit symbols to their corresponding IDs that gets used in later data import functions.

Returns:

Dictionary that maps gene/transcription unit symbols to gene/transcription unit IDs used by the model. all_gene_ids: Set of all gene IDs used by the model.

Return type:

symbols_to_ids