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[source]

Bases: object

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

Bases: object

Parameters:

  • operons_on (bool) –

  • remove_rrna_operons (bool) –

  • remove_rrff (bool) –

  • new_genes_option (str) –

_check_new_gene_ids(nested_attr)[source]

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

_get_new_gene_sequence(nested_attr)[source]

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

_join_data()[source]

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

_load_parameters(file_path)[source]
_load_sequence(file_path)[source]
_load_tsv(dir_name, file_name)[source]
_modify_data()[source]

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()[source]

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)[source]

Update insertion location of new genes to prevent conflicts.

_update_gene_locations(nested_attr, insert_pos)[source]

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