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fasta_split.py
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fasta_split.py
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#!/usr/bin/env python
"""Split a fasta file in n files of approximately the same number of sequences
WARNING: This will create 'n' files in your present directory
USAGE:
python fasta_split.py input_file num_files
input_file: fasta file
num_files: number of files to split into
"""
# Importing modules
import sys
# Defining classes
class Fasta(object):
"""Fasta object with name and sequence
"""
def __init__(self, name, sequence):
self.name = name
self.sequence = sequence
def write_to_file(self, handle):
handle.write(">" + self.name + "\n")
handle.write(self.sequence + "\n")
# Defining functions
def fasta_iterator(input_file):
"""Takes a fasta file input_file and returns a fasta iterator
"""
with open(input_file) as f:
sequence = ""
name = ""
begun = False
for line in f:
line = line.strip()
if line.startswith(">"):
if begun:
yield Fasta(name, sequence)
name = line.replace(">", "")
sequence = ""
begun = True
else:
sequence += line
yield Fasta(name, sequence)
if __name__ == '__main__':
try:
input_file = sys.argv[1]
num_files = int(sys.argv[2])
except:
print __doc__
sys.exit(1)
# Open output files for writting
#output_files = {}
#for n in xrange(1, num_files + 1):
# output_files[n] = open(input_file + str(n) + ".fasta", "w")
# Iterate through sequences and write to files
file_number = 0
for sequence in fasta_iterator(input_file):
n = file_number % num_files + 1
current_file = input_file + str(n) + ".fasta"
with open(current_file, "a") as f:
sequence.write_to_file(f)
file_number += 1