reconstruction.ecoli.knowledge_base_raw

KnowledgeBase for Ecoli Whole-cell knowledge base for Ecoli. Contains all raw, un-fit data processed directly from CSV flat files.

class reconstruction.ecoli.knowledge_base_raw.DataStore

Bases: object

class reconstruction.ecoli.knowledge_base_raw.KnowledgeBaseEcoli(operons_on, remove_rrna_operons, remove_rrff, stable_rrna, new_genes_option='off')

Bases: object

Parameters:

• operons_on (bool)

• remove_rrna_operons (bool)

• remove_rrff (bool)

• stable_rrna (bool)

• new_genes_option (str)

_check_new_gene_ids(nested_attr)

Check to ensure each new gene, RNA, and protein id starts with NG.

_get_new_gene_sequence(nested_attr)

Determine genome sequnce for insertion using the sequences and relative locations of the new genes.

_join_data()

Add rows that are specified in additional files. Data will only be added if all the loaded columns from both datasets match.

_load_parameters(dir_name, file_name)

_load_sequence(file_path)

_load_tsv(dir_name, file_name)

_modify_data()

Modify entires in rows that are specified to be modified. Rows must be identified by their entries in the first column (usually the ID column).

_prune_data()

Remove rows that are specified to be removed. Data will only be removed if all data in a row in the file specifying rows to be removed matches the same columns in the raw data file.

_update_gene_insertion_location(nested_attr)

Update insertion location of new genes to prevent conflicts.

_update_gene_locations(nested_attr, insert_pos)

Modify positions of original genes based upon the insertion location of new genes. Returns end position of the gene insertion.

_update_global_coordinates(data, insert_pos, insert_len)

Updates the left and right end positions for all elements in data if their positions will be impacted by the new gene insertion.

Parameters:

• data – Data attribute to update

• insert_pos – Location of new gene insertion

• insert_len – Length of new gene insertion