Cookbook

Sequence Cleaner

Description

I want to share my script using Biopython to clean sequences up. You should know that 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 it allows ) and in the end the user can choose if he/she wants to have a file as output or print the result.

Script

import sys
from Bio import SeqIO


def sequence_cleaner(fasta_file, min_length=0, por_n=100):
    # Create our hash table to add the sequences
    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
        sequence = str(seq_record.seq).upper()
        # 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 isn't in the
            # hash table, the sequence and its id are going to be in the hash
            if sequence not in sequences:
                sequences[sequence] = seq_record.id
            # 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
            else:
                sequences[sequence] += "_" + seq_record.id

    # Write the clean sequences

    # Create a file in the same directory where you ran this script
    with open("clear_" + fasta_file, "w+") as output_file:
        # Just read the hash table and write on the file as a fasta format
        for sequence in sequences:
            output_file.write(">" + sequences[sequence] + "\n" + sequence + "\n")

    print("CLEAN!!!\nPlease check clear_" + fasta_file)


userParameters = sys.argv[1:]

try:
    if len(userParameters) == 1:
        sequence_cleaner(userParameters[0])
    elif len(userParameters) == 2:
        sequence_cleaner(userParameters[0], float(userParameters[1]))
    elif len(userParameters) == 3:
        sequence_cleaner(
            userParameters[0], float(userParameters[1]), float(userParameters[2])
        )
    else:
        print("There is a problem!")
except:
    print("There is a problem!")

Using the command line, you should run:

python sequence_cleaner.py input[1] min_length[2] min[3]

There are 3 basic parameters:

[1]: your fasta file
[2]: the user defines the minimum length. Default value 0, it means you don’t have to care about the minimum length
[3]: the user defines the % of N is allowed. Default value 100, all sequences with ’N’ will be in your ouput, set value to 0 if you want no sequences with ”N” in your output

For example:

python sequence_cleaner.py Aip_coral.fasta 10 10

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

Questions, Suggestions or Improvement

Send an email to genivaldo.gueiros@gmail.com