renamer.py

#~ standard library imports
import sys
import re

#~ local file import (the dict of codes:species)
try:
    import species_dict
except Exception as e:
    print(f"You'll need your codes:species dict here, named \"species_dict.py\"\n"
          f"or there is an issue: {e}")
    sys.exit(1)

#~ check for arg (the file to convert)
if len(sys.argv) != 2:
    print("Please provide a file to convert, for example:")
    print("python renamer.py tree1")
    sys.exit(1)

#~ open the file, call it "infile"
with open(sys.argv[1]) as infile:
    #~ read the lines into a variable called "newick"
    newick = infile.read()

#~ create hit counter
hits = 0
for code in species_dict.spec_dict:
    #~ check if code exists in tree
    if re.search(code, newick):
        #~ if so, replace code with species
        newick = re.sub(code, species_dict.spec_dict[code], newick)
        hits += 1 #~ increment counter

#~ make an output file to write to, prefix name with "renamed_"
with open(f"renamed_{sys.argv[1]}", "w") as outfile:
    outfile.write(newick)
    print(f"OK, {hits} nodes renamed in {sys.argv[1]}, written to renamed_{sys.argv[1]}")