/
reformat-fasta.py
executable file
·89 lines (78 loc) · 2.83 KB
/
reformat-fasta.py
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from collections import defaultdict
import re, os
import textwrap
import argparse
import sys
parser = argparse.ArgumentParser(
prog="reformat-fasta",
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''
Program for reformatting fasta file alla Anvi'o
'''))
parser.add_argument('-i', help='input fasta file')
parser.add_argument('-o', help="output re-formatted fasta file")
parser.add_argument('-min_length', help="minimum sequence length for fasta file")
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
args = parser.parse_known_args()[0]
def stabilityCounter(int):
if len(str(int)) == 1:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 2:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 3:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 4:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 5:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 6:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 7:
string = (str(0) + str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 8:
string = (str(0) + str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 9:
string = (str(0) + str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 10:
string = (str(0) + str(0) + str(int))
return (string)
if len(str(int)) == 11:
string = (str(0) + str(int))
return (string)
def fasta(fasta_file):
outfile = open(args.o, "w")
seq = ''
header = ''
count = 0
for i in fasta_file:
i = i.rstrip()
if re.match(r'^>', i):
if len(seq) >= int(args.min_length):
outfile.write(">" + header + "\n")
outfile.write(seq + "\n")
count += 1
headerNum = stabilityCounter(count)
header = ("c_" + str(headerNum))
seq = ''
else:
count += 1
headerNum = stabilityCounter(count)
header = ("c_" + str(headerNum))
seq = ''
else:
seq += i
outfile.write(">" + header + "\n")
outfile.write(seq + "\n")
file = open(args.i, "r")
fasta(file)