pandas - Overwrite header of fasta file with a column value, by matching the file name with part of the column value

Question

Dataset:

Submitter | Filename | Virus

Lyn | 012345.fasta | abc/USA/abc-01234567/1234

Lyn | 012345.fasta | abc/USA/abc- 04567898/1234

Lyn | 012345.fasta | abc/USAabc- 78935421/1234

Files within a directory called 012345:

04567898-abc-a124-pol.fasta

78935421-abc-a124-pol.fasta

01234567-abc-a124-pol.fasta

Inside of a file:

&01234567-abc-a124-pol

ACTGATGATGAGATAGA ATAGATAGATAGATAG

AGATAGATAGATA

Note: there is the same 8 digit number within Column C, a fasta file name, and the fasta file header.

What I want to do is take the entire string from Column C, and overwrite the current fasta file header. The output would look like this:

Fasta file name:

01234567-abc-a124-pol.fasta

Inside of a file:

&abc/USA/abc-01234567/1234

ACTGATGATGAGATAGA ATAGATAGATAGATAG

AGATAGATAGATA

Here is a class I am trying to write to do that. I am struggling to get it to work. Please let me know if there is a simpler way.

def parse(file_name):   
    with zipfile.ZipFile(file_name, "r") as zf:
        for name in zf.namelist():
            if ".fasta" in str(name) and '.ipynb' not in str(name):
                with io.TextIOWrapper(zf.open(name)) as file:
                    e = "".join([">{} 
{}".format(str(title.split(None, 1)[0]), identifiers)
                        for title, identifiers in SimpleFastaParser(file)])
                with open("test_dict.fasta", "a+") as f0:
                    f0.write('{}
'.format(e))
    return file_name       

def names(file_name):
    with zipfile.ZipFile(file_name, "r") as zf:
        e1 = []
        for name in zf.namelist():
            if ".fasta" in str(name) and '.ipynb' not in str(name):
                with io.TextIOWrapper(zf.open(name)) as file:
                    e1 += [title.split(None, 1)[0]
                        for title, identifiers in SimpleFastaParser(file)]
        print(e1)
        return 

def pandas(file_name):
    with zipfile.ZipFile(file_name, "r") as zf:
        e4 = []
        for name in zf.namelist():
            if ".fasta" in str(name) and '.ipynb' not in str(name):
                with io.TextIOWrapper(zf.open(name)) as file:
                    e4 += [{title.split(None, 1)[0]:[identifiers, len("".join(identifiers))]
                        for title, identifiers in SimpleFastaParser(file)}]

                          
                dataset = pd.DataFrame({'Name': ["".join(i.keys()) for i in e4], 
                                        'Length':[list(i.values())[0][1] for i in e4],
                                        'Sequence':[list(i.values())[0][0] for i in e4]})
                   
            
        return dataset

question from:https://stackoverflow.com/questions/65833365/overwrite-header-of-fasta-file-with-a-column-value-by-matching-the-file-name-wi

Answer 1

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