fastq_min_max_length.py

#!/usr/bin/env python
"""Keep only sequences that have a length between a min and a max values

Usage:
    python fastq_min_length.py input_file minimum maximum output_file

input_file = input compressed Fastq file
minimum = minimum length accepted (inclusive)
maximum = maximum length accepted (inclusive)
output_file = output Fastq file
"""

# Importing modules
import gzip
import sys

# Defining classes
class Fastq(object):
    """Fastq object with name and sequence
    """
    def __init__(self, name, seq, name2, qual):
        self.name = name
        self.seq = seq
        self.name2 = name2
        self.qual = qual
    def write_to_file(self, handle):
        handle.write("@" + self.name + "\n")
        handle.write(self.seq + "\n")
        handle.write("+" + self.name2 + "\n")
        handle.write(self.qual + "\n")

# Defining functions
def fastq_parser(input_file):
    """Takes a fastq file infile and returns a fastq object iterator
    """
    with gzip.open(input_file, "rb") as f:
        while True:
            name = f.readline().strip()[1:]
            if not name:
                break
            seq = f.readline().strip()
            name2 = f.readline().strip()[1:]
            qual = f.readline().strip()
            yield Fastq(name, seq, name2, qual)

# Main
if __name__ == '__main__':
    try:
        input_file = sys.argv[1]
        minimum = int(sys.argv[2])
        maximum = int(sys.argv[3])
        output_file = sys.argv[4]
    except:
        print __doc__
        exit(1)

    assert minimum >= 1, "minimum must be a positive integer"
    assert maximum >= 1, "maximum must be a positive integer"

    # Filter sequences
    sequences = fastq_parser(input_file)
    with gzip.open(output_file, "wb") as out_f:
        for s in sequences:
            if len(s.seq) >= minimum and len(s.seq) <= maximum:
                s.write_to_file(out_f)