Sequence Cleaner

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I want to share my script using biopython to clean sequences up , you should know analyzing poor data takes CPU time and interpreting the results from poor data takes people time, so it's always important to make a preprocessing.

Let me call my script as “Sequence_cleaner” and the big idea is to remove duplicate sequences, remove too short sequences ( the user defines the minimum length) and remove sequences which have too many unknown nucleotides (N) ( the user defines the % of N is allows ) and in the end the user can choose if he/she wants to have a file as output or print the result.


from Bio import SeqIO
def sequence_cleaner(fasta_file,min_length=0,por_n=100):
    #create our hash table to add the sequences
    #Using the biopython fasta parse we can read our fasta input
    for seq_record in SeqIO.parse(fasta_file, "fasta"):
        #Take the current sequence
        #Check if the current sequence is according to the user parameters
        if (len(sequence)>=min_length and (float(sequence.count("N"))/float(len(sequence)))*100<=por_n):
       # If the sequence passed in the test "is It clean?" and It isnt in the hash table , the sequence and Its id are going to be in the hash
            if sequence not in sequences:
       #If It is already in the hash table, We're just gonna concatenate the ID of the current sequence to another one that is already in the hash table
    #Write the clean sequences
    #Create a file in the same directory where you ran this script
    #Just Read the Hash Table and write on the file as a fasta format
    for sequence in sequences:

You should call the function 'sequence_cleaner', there are 3 basic parameters:

        #1st: your fasta file 
        #2nd: the user defines the minimum length (default value 0 ( It means you don't have to care about the minimum lenght)
        #3rd: the user defines the % of N is allowed (default value 100 ( It means  you dont care to 'N' in your sequences))

FYI if you don't care about the 2nd and the 3rd parameters you are just gonna remove the duplicate sequences

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