#Python scripts contained in this folder only work under the following system
#Supporting OS: CentOS7 
#Supporting python version: python2.7
#Required python library: wxpython (>ver. 4.0.1), numpy, Biopython (>1.71)
#Required software: clustalw (version 2.0.10 or 2.1)


Procedure how to run the scripts
1. Install python library (wx, numpy and Biopython) by open source management system, such as Conda.

2. Install clustalw software.

3. Download homologous sequences of target protein from Blastp web server.

4. (command line) Input following command: python Library_GUI_from_161003.py

5. (From GUI at 1st line) Select the input file downloaded from Blastp from the tab written as "dir..."

6. (From GUI at 2nd line) enter the output file name from the tab written as "dir..."

7. (From GUI) click "OK" button to run the script.

8. (From GUI) Turn off the GUI.

9. (Command line) Input the following command: python Library_lscut.py -INPUTSTP <file name containing target protein sequence> -INPUTLIB <library file generated after proc. 7> -CUTPER <number> -OUTPUT <output file name>
#Example: python Library_lscut.py -INPUTSTP test/EcBirA -INPUTLIB test/BirA-5000seqs-1E-5.out -CUTPER 0.05 -OUTPUT test/5cut.txt -> By running this script, sequences having < 304 (less than 95% of sequence length of BirA) and > 337 (ess than 105% of sequence length of BirA) residues in test/BirA-5000seqs-1E-5.out were omitted and saved as test/5cut.txt.

10. (Command line) Input the following command: python -LIBRARY <library file generated after proc. 9> -CLUSTALPATH <path to clustalw2 executable file> -CUTNUM <numbers from 0 to 100> -OUTPUT <output file name>
#Example: python Library_overlap_deleter.py -LIBRARY test/5cut.txt -CLUSTALPATH ../../clustalw-2.1/src/clustalw2 -CUTNUM 90.0 -OUTPUT test/5cut-90per.txt -> By running this script, sequences bearing >90% identity each other in the test/5cut.txt were omitted and saved as <output file name>. To figure out detail algorithm, please check the Supporting information of Fig. 1 of the following paper: Shogo Nakano et al., (2019), Appl. Env. Microbiol., DOI: 10.1128/AEM.00459-19.
