Using Biopython SeqIO.convert over an entire directory
Question: I have 51 files with metagenomic sequence data that I would like to convert
from fastq to fasta using a Biopython script in Windows. The module
SeqIO.convert easily converts an individually specified file, but I can't
figure out how to convert the entire directory. It's not really too many files
to do individually, but I'm trying to learn.

I'm brand new to Biopython, so please forgive my ignorance. [This
convo](http://stackoverflow.com/questions/21743438/how-do-i-pass-biopython-
seqio-convert-over-multiple-files-in-a-directory) was helpful, but I'm still
not able to convert the directory from fastq to fasta.

Here's the code I've been trying to run:

    
    
    #modules- 
    import sys
    import re
    import os
    import fileinput
    
    from Bio import SeqIO
    
    #define directory
    Directory = "FastQ”
    
    #convert files  
    def process(filename):
      return SeqIO.convert(filename, "fastq", "files.fa", filename + ".fasta",   "fasta", alphabet= IUPAC.ambiguous_dna)
    


Answer: You need to iterate over the files in the directory and convert them, so
assuming your directory is `FastQ` and that you are calling your script from
the proper folder (i.e. the one that your directory is in, since you are using
a relative path), you would need to do something like:

    
    
    def process(directory):
        filelist = os.listdir(directory)
        for f in filelist:
            SeqIO.convert(f, "fastq", f.replace(".fastq",".fasta"), "fasta", alphabet= IUPAC.ambiguous_dna)
    

then you would call your script in your main:

    
    
     my_directory = "FastQ"
     process(my_directory)
    

I think that should work.

