parse_excel

Defines functions for parsing data directly from Excel in specific formats.

neutcurve.parse_excel.parseRachelStyle2019(*, excelfile, sheet_mapping)

Parse data from Rachel Eguia’s 2019-style assays on Bloom lab Tecan.

Args:

excelfile (str)

Excel file with data exactly as produced by plate reader.

sheet_mapping (dict)

Describes data in each sheet of excelfile. There should be a key matching the name of each Excel sheet. The value for each key is another dict with the following keys / values describing the data for that plate (we assume one sheet per serum / virus pair):

• ‘serum’: name of serum.

• ‘virus’: name of virus.

• ‘dilution_factor’: fold-dilution of serum along plate.

• ‘initial_concentration’: serum concentration in first well used to start dilution series.

• ‘excluded_dilutions’ (optional) : list of dilutions to exclude from returned results, with 1 being least dilute and 12 being most dilute. Useful if some columns in plate have a known problem.

Returns:

A pandas DataFrame in the tidy format read by neutcurve.curvefits.CurveFits.