geckopy.experimental.molecular_weights

Build dataframe with protein reactions identifiers, Uniprot IDs and MW.

Module Contents

Functions

get_uniprot(query: str) → str	Get uniprot information corresponding to a query.
parse_mw(uniprot_info: str) → str	Get all MW of uniprot text (Dalton).
extract_proteins(model, all_proteins: Optional[Dict] = None, key_fn=lambda x: UNIPROT_PATTERN.match(x.id)[1]) → pandas.DataFrame	Generate the dataframe protein reactions IDs, Uniprot IDs and MW.

geckopy.experimental.molecular_weights.get_uniprot(query: str) → str

Get uniprot information corresponding to a query.

Parameters

query (str) – an UNIPROT ID(s), separated by spaces

geckopy.experimental.molecular_weights.parse_mw(uniprot_info: str) → str

Get all MW of uniprot text (Dalton).

geckopy.experimental.molecular_weights.extract_proteins(model, all_proteins: Optional[Dict] = None, key_fn=lambda x: ...) → pandas.DataFrame

Generate the dataframe protein reactions IDs, Uniprot IDs and MW.

Parameters

• model (cobra.Model) –

• all_proteins (dict) – dict of UNIPROT IDs to protein reaction identifiers as in the model. If None are supplied, the function will try to identify them with a simple regex.

• key_fn (function) – mapping to extract the uniprot id from the protein. Default: regex matching on the protein id.

Returns

df

Return type

pd.DataFrame