序列清理器

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!")