msions.encyclopedia

This module contains functions that are useful for interacting with EncyclopeDIA files in Python.

Module Contents

Functions

dia_df(→ pandas.DataFrame)

Create a pandas DataFrame from an EncyclopeDIA elib output

match_hk(→ int)

Match EncyclopeDIA elib output to Hardklor output
msions.encyclopedia.dia_df(input_elib: str) → pandas.DataFrame[source]

Create a pandas DataFrame from an EncyclopeDIA elib output

Parameters:

input_elib (str) – The input elib file.

Returns:

A pandas DataFrame containing PrecursorMz, PrecursorCharge, PeptideModSeq, PeptideSeq, RtInSeconds, RTInSecondsStart, and RTInSecondsStop columns.

Return type:

pd.DataFrame

Examples

>>> from msions.encyclopedia import dia_df
>>> dia_df("test.elib")
msions.encyclopedia.match_hk(ref_row: pandas.Series, other_df: pandas.DataFrame) → int[source]

Match EncyclopeDIA elib output to Hardklor output

Parameters:

  • ref_row (pd.Series) – The row of data to match.

  • other_df (pd.DataFrame) – The other DataFrame to match.

Returns:

Number of rows in match DataFrame.

Return type:

int

Examples

>>> from msions.encyclopedia import match_hk
>>> import msions.hardklor as hk
>>> import msions.encyclopedia as encyclo
>>> hk_df = hk.hk2df("test.hk")
>>> encyclo_df = encyclo.dia_df("test.elib")
>>> hk_df["in_encyclo"] = hk_df.apply(match_hk, axis=1, other_df=encyclo_df)