串联来自不同文件夹的fasta文件

Question

I have a large numbers of fasta files (these are just text files) in different subfolders. What I need is a way to search through the directories for files that have the same name and concatenate these into a file with the name of the input files. I can't do this manually as I have 10000+ genes that I need to do this for.

So far I have the following Python code that looks through one of the directories and then uses those file names to search through the other directories. This returns a list that has the full path for each file.

    import os
    from os.path import join, abspath

    path = '/directoryforfilelist/'    #Directory for source list
    listing = os.listdir(path)

    for x in listing:
        for root, dirs, files in os.walk('/rootdirectorytosearch/'):
            if x in files:
            pathlist = abspath(join(root,x))

Where I am stuck is how to concatenate the files it returns that have the same name. The results from this script look like this.

    /directory1/file1.fasta
    /directory2/file1.fasta
    /directory3/file1.fasta
    /directory1/file2.fasta
    /directory2/file2.fasta
    /directory3/file2.fasta

In this case I would need the end result to be two files named file1.fasta and file2.fasta that contain the text from each of the same named files.

Any leads on where to go from here would be appreciated. While I did this part in Python anyway that gets the job done is fine with me. This is being run on a Mac if that matters.

Answer 1

For each file of your list, allocate the target file in append mode, read each line of your source file and write it to the target file.

Assuming that the target folder is empty to start with, and is not in /rootdirectorytosearch.

Answer 2

Not tested, but here's roughly what I'd do:

from itertools import groupby
import os

def conc_by_name(names):
    for tail, group in groupby(names, key=os.path.split):
        with open(tail, 'w') as out:
           for name in group:
              with open(name) as f:
                  out.writelines(f)

This will create the files ( file1.fasta and file2.fasta in your example) in the current folder.