Input/Output (IO)

padua.io.read_maxquant(f, header=0, index_col='id', **kwargs)

Load the quantified table output from MaxQuant run, e.g.

• Proteingroups.txt
• Phospho (STY)Sites.txt

Parameters:f – Source file Returns:Pandas dataframe of imported data

padua.io.read_perseus(f)

Load a Perseus processed data table

Parameters:f – Source file Returns:Pandas dataframe of imported data

padua.io.write_perseus(f, df)

Export a dataframe to Perseus; recreating the format

Parameters:

• f –
• df –

Returns:

padua.io.write_phosphopath(df, f, extra_columns=None)

Write out the data frame of phosphosites in the following format:

protein, protein-Rsite, Rsite, multiplicity
Q13619  Q13619-S10      S10     1
Q9H3Z4  Q9H3Z4-S10      S10     1
Q6GQQ9  Q6GQQ9-S100     S100    1
Q86YP4  Q86YP4-S100     S100    1
Q9H307  Q9H307-S100     S100    1
Q8NEY1  Q8NEY1-S1000    S1000   1

The file is written as a comma-separated (CSV) file to file f.

Parameters:

• df –
• f –

Returns:

padua.io.write_phosphopath_ratio(df, f, v, a=None, b=None)

Write out the data frame ratio between two groups protein-Rsite-multiplicity-timepoint ID Ratio Q13619-S10-1-1 0.5 Q9H3Z4-S10-1-1 0.502 Q6GQQ9-S100-1-1 0.504 Q86YP4-S100-1-1 0.506 Q9H307-S100-1-1 0.508 Q8NEY1-S1000-1-1 0.51 Q13541-S101-1-1 0.512 O95785-S1012-2-1 0.514 O95785-S1017-2-1 0.516 Q9Y4G8-S1022-1-1 0.518 P35658-S1023-1-1 0.52

Parameters:

• df –
• f –
• v – Value ratio
• t – Timepoint
• a –
• b –

Returns:

padua.io.write_r(df, f, sep=', ', index_join='@', columns_join='.')

Export dataframe in a format easily importable to R

Index fields are joined with “@” and column fields by ”.” by default. :param df: :param f: :param index_join: :param columns_join: :return: