filterframes 0.1.1

A very simple DTASelect-Filter.txt parser.

pandas-dta-select-parser

pandas_dta_select_parser is a Python package that provides an easy way to parse and manipulate DTASelect filter files using pandas. The package allows you to read DTASelect-filter.txt files, create peptide and protein dataframes, modify the dataframes, and write the modified dataframes back to a new DTASelect-filter.txt file. Additional utility functions are provided for common tasks, such as filtering, normalization, and peptide coverage calculation.

Installation

You can install pandas_dta_select_parser using pip:

pip install pandas-dta-select-parser

Usage

Here's a basic example of how to use the package:

from filterframes import from_dta_select_filter, to_dta_select_filter

# Read DTASelect-filter.txt file and create peptide and protein dataframes
file_input = "path/to/DTASelect-filter.txt"
header_lines, peptide_df, protein_df, end_lines = from_dta_select_filter(file_input)

# Modify peptide or protein dataframes as needed (e.g., filtering, normalization, etc.)
# ...

# Write modified peptide and protein dataframes back to a DTASelect-filter.txt file
file_output = "path/to/output/DTASelect-filter_modified.txt"
with open(file_output, 'w') as f:
    output_string_io = to_dta_select_filter(header_lines, peptide_df, protein_df, end_lines)
    f.write(output_string_io.getvalue())

More advance use cases can be found in examples.py

Functions

The main functions provided by the package are:

from_dta_select_filter(file_input: Union[str, TextIOWrapper, StringIO]) -> Tuple[List[str], pd.DataFrame, pd.DataFrame, List[str]]

Reads a DTASelect-filter.txt file and returns header lines, peptide dataframe, protein dataframe, and end lines.

to_dta_select_filter(header_lines: List[str], peptide_df: pd.DataFrame, protein_df: pd.DataFrame, end_lines: List[str]) -> StringIO

Writes the given header lines, peptide dataframe, protein dataframe, and end lines to a StringIO object in the DTASelect-filter.txt format.