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import sys
import argparse
class FQRecord:
def __init__(self):
self.seq = ""
self.qual = ""
self.anno = ""
self.name = ""
def string(self):
ret = "@" + self.name.strip() + "\n" + \
self.seq + "\n" + \
"+" + self.anno + "\n" + \
self.qual
return ret
"""Takes in a pseudo fasta and makes a
pseudo fastq from it"""
def make_fastq(record, name, fake_qual, seq="", anno=""):
if record.name == "":
record.name = name
record.qual = "".join([fake_qual for i in range(0, len(record.seq))])
return record
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument("-i", dest="infile", type=str, required=True)
parser.add_argument("-n", dest="namebase", type=str, required=True)
parser.add_argument("-q", dest="qual", type=str, required=True)
return parser.parse_args()
if __name__ == "__main__":
## Add the sample name to the front of the
## read line.
args = parse_args()
readfile = args.infile
name_base = args.namebase
fake_qual = args.qual
count = 0
with open(readfile, "r") as fi:
for line in fi:
record = FQRecord()
record.seq = line.strip()
record.name = name_base + "_" + str(count)
record = make_fastq(record, "", fake_qual)
print(record.string())
count += 1
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