XMAn_nonmutated_peptides

This script eliminates the hits reported from protein identification tools (proteomics) without the mutated amino acid in the sequence.

Input

1. A file in EXCEL format (.xlsx) containing any columns but 2 columns with the exact following names: Sequence and Protein Descriptions.
   • Sequence column contains the hit sequences reported by the protein identification tool.
   • Protein Descriptions contains the descriptions of the hits and these need to include the short sequence from the XMAn.v2 headers. (e.g. GN=CDC42BPB MRCKB_HUMAN Serine/threonine-protein kinase MRCK beta|c_C3625A|p_L1209I|VGIIEGL|Missense)

Dependencies

pandas

openpyxl

xlrd

Usage

Linux/Mac

Install dependencies with pip:

$ pip install pandas

$ pip install xlrd

$ pip install openpyxl

$ git clone https://github.com/lazarlab/XMAn-v2.git

$ cd XMAn-v2/

$ python eliminate_nonmut_peptides.py protein_id_excel_filename output_filename

Windows

download python (https://www.python.org/downloads/)

Go to windows start and in search type 'cmd' and click to open

Type the following commands followed by enter to install dependencies:

$ pip install pandas

$ pip install xlrd

$ pip install openpyxl

download this repository as a zip folder under the green botton "Clone or download"

unzip the folder

Type the following commands followed by enter to run the script:

$ cd PathToDownloadedRepository\XMan-v2-master (if in Downloads type cd Downloads\XMan-v2-master\XMan-v2-master)

$ python eliminate_nonmut_peptides.py <input_filename>.xlsx <output_filename>.xlsx