replace.py

#fin1 X aa, fin2 nultide,fout1 new file 

#! /bin/python
with open(r"/home/bowen/AzoFC2-heterodimer/20_select/re-name/aa.fasta", "r") as fin1:
    with open(r"/home/bowen/AzoFC2-heterodimer/20_select/re-name/aa-nul-final-3", "w") as fout1:
        with open(r"/home/bowen/AzoFC2-heterodimer/20_select/re-name/aa-nul.fasta", "r") as fin2:
            # part 1
            seq_name = []
            char_index = []
            for line in fin1.readlines():
                line = line.strip()
                if line.startswith(">"):
                    seq_name.append(line.split(">")[1])
                else:
                    char_index.append([index for index, char in enumerate(line) if char == 'F'])
            seq_char_index = dict(zip(seq_name, char_index))
            seq_char_index = {k: v for k, v in seq_char_index.items() if len(v) != 0}

            # part 2
            seq_name = []
            seq_info = []
            for line in fin2.readlines():
                line = line.strip()
                if line.startswith(">"):
                    seq_name.append(line.split(">")[1])
                else:
                    seq_info.append([line[i:i+3] for i in range(0, len(line), 3)])
            seq_info = dict(zip(seq_name, seq_info))

            for key, value in seq_info.items():
                if key not in seq_char_index.keys():
                    seq_info[key] = [x if x not in ["TTC", "TTT"] else "TAG" for x in value]
                else:
                    for index, codon in enumerate(value):
                        if codon in ["TTC", "TTT"] and index not in seq_char_index[key]:
                            seq_info[key][index] = "TAG" 

            for key, value in seq_info.items():
                fout1.write(">" + str(key) + "\n")
                fout1.write(''.join([x for x in value]) + "\n")