-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathfastq_to_fasta.py
executable file
·42 lines (33 loc) · 2.24 KB
/
fastq_to_fasta.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
#!/usr/bin/env python
#######################################################################################
### ###
### Copyright (C) 2018 Pawel Krawczyk ([email protected]) ###
### ###
### This program is free software: you can redistribute it and/or modify ###
### it under the terms of the GNU General Public License as published by ###
### the Free Software Foundation, either version 3 of the License, or ###
### (at your option) any later version. ###
### ###
### This program is distributed in the hope that it will be useful, ###
### but WITHOUT ANY WARRANTY; without even the implied warranty of ###
### MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ###
### GNU General Public License for more details. ###
### ###
### You should have received a copy of the GNU General Public License ###
### along with this program. If not, see <http://www.gnu.org/licenses/>. ###
### ###
#######################################################################################
from Bio import SeqIO
import argparse
parser = argparse.ArgumentParser(
description='Convert fastq to fasta')
parser.add_argument('--input', dest='inputfile', action='store',
help='Input fastq file (required)', required=True)
parser.add_argument('--output', dest='outputfile', action='store',
help='Output fasta file (required)', required=True)
args = parser.parse_args()
with open(args.inputfile, "rU") as input_handle:
with open(args.outputfile,"w") as output_handle:
sequences = SeqIO.parse(input_handle, "fastq")
count = SeqIO.write(sequences, output_handle, "fasta")
print("Converted %i records" % count)