SCAProtein

Search, concatenate and alignment of protein sequences

Prerequired softwares

Make sure python and biopython are installed.

To install biopython:

	pip install biopython

and if you do not have sudo authority, try:

	pip install --user biopython 

Download and Run

After download and decompress, run the following command to make sure the multiple sequence alignment tool can run:

	chmod +x muscle3.8.31_i86linux64

Configuration (set the parameters at config.txt):

	BatchSize 5000     #Batch size when fetch
	
	RetMax 10000       #How many records in all will be fetched from NCBI
	
	N_Threads 4        #Number of threads
	
	WindowSize 15      #When kick out species, the window size to check gap
	
	N_Species_Gap 1    #If there is only N_Species_Gap species have value, other are all gap, then these N_Species_Gap species will be removed

To run the program:

	python main.py Options subtrate_term_file subunit_term_file subtrate_cleave_file subunit_cleave_file

	Options:

						fetch          Fetch from NCBI by give list
						
						cleave         Cleave pre-seq
						
						convert        Convert plain txt to fasta
						
						cat            Concatenate sequences

						align          Run multiple sequence alignment
						
						kick           Kick out the badly aligned sequences
						
						realign        Re-run multiple sequence alignment after kicking
						
						all            Run the whole pipeline

						clear          Clear all old files

Sample usage:

python main.py all subtrate.list subunit.list subtrate_cleave.list subunit_cleave.list