Was getting some No such directory errors and was able to figure out how to modify the code so it would work (using MacOS system). Code below. Running it only replaces some of the targeted headers, specifically it seems to only replace those formatted that have Clavigralla and Anoplocnemis. I think I see why and will play with the script some more.
#!/usr/bin/env python
# Replace header inoriginal file header with header in header file, writing output to outputfile
# Larz60+
# from pathlib import Path
import os
import sys
import argparse
class SwapHeaders:
def __init__(self, origfile=None, headerfile=None, outfile=None):
# Note Modern pathlib objects removed because they won't work in
# outdated python 2.7
# self.home = Path('.')
# self.data = self.home / 'data'
# self.original_file = self.data / origfile
# self.header_file = self.data / headerfile
# self.out_file = self.data / outfi
# with self.header_file.open() as fh:
# self.header_data = fh.readlines()
# self.orig = self.original_file.open()
# self.fo = self.out_file.open('w')
self.home = os.getcwd()
self.data = self.home + '/data/'
self.original_file = self.data + origfile
self.header_file = self.data + headerfile
self.out_file = self.data + outfile
with open(self.header_file, 'r') as fh:
self.header_data = fh.readlines()
self.orig = open(self.original_file, 'r')
self.fo = None
def close_files(self):
self.orig.close()
def get_replacement_header(self, match):
retrec = None
for line in self.header_data:
if not line.startswith('>'):
continue
if match in line:
retrec = line
break
return retrec
def read_orig_record(self):
"""
original file record read
:return: data or False
"""
while True:
data = self.orig.readline()
if not data:
break
yield data
def make_new_file(self):
# with self.out_file.open('w') as fo:
with open(self.out_file, 'w') as fo:
for orig in self.read_orig_record():
match = None
if orig.startswith('>'):
match = orig[1:]
x = match.rfind('.')
if x:
match = match[:x]
new = self.get_replacement_header(match)
if new is not None:
fo.write(new)
else:
fo.write(orig)
else:
fo.write(orig)
def main():
# Typical command line call python SwapHeaders.py -i 'File1.txt' -b 'File2.txt' -o 'Fileout.txt'
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--ifile",
dest='original_filename',
help="Filename where headers are to be replaced",
action="store")
parser.add_argument("-b", "--bfile",
dest='replace_original_filename',
help="Filename containing body",
action="store")
parser.add_argument("-o", "--ofile",
dest='out_filename',
help="Output filename",
action="store")
args = parser.parse_args()
original_filename = args.original_filename
replace_original_filename = args.replace_original_filename
out_filename = args.out_filename
sh = SwapHeaders(origfile=original_filename, headerfile=replace_original_filename, outfile=out_filename)
sh.make_new_file()
sh.close_files()
if __name__ == '__main__':
main()
If I change line 70 'x = match.rfind('.')' to 'x = match.rfind('seq1')', that certainly will select the other targeted headers, but it will include headers that have, e.g., 'seq1_A_' and 'seq1_B_' which I do not want to include. Is there a way to get the match.rfind search term to exclude these instances or to just include seq1_[some numerical digits]?
