rotifer.db.methods.IPGCursor

class rotifer.db.methods.IPGCursor

Bases: object

Mixin for cursors that return identical protein group reports.

Identical protein group (IPG) reports are tables that list, for each queried protein, all identical sequences known to NCBI together with their genomic coordinates.

getids(obj)

Extract protein accessions from IPG dataframes.

Parameters:

objpandas.DataFrame or list of pandas.DataFrame

IPG reports produced by the cursor.

Returns:

set of str

All accessions in the pid and representative columns.

property columns

Column names of the IPG dataframe.

Returns:

list of str

The original NCBI report columns followed by the columns added by rotifer (order, is_query and representative).