[BioPython] suggestion on Fasta.index_file()

[CL WU]

I see. I think giving a optional filename argument is more flexible.

Thanks, Brad.

Chunlei

Brad Chapman wrote:

>Hi Chunlei;
>
>  
>
>>However, the generated index file stores the absolute path for 
>>fasta_seq_file,
>>    
>>
>
>It should just store the filename for whatever you pass to the
>index_file function. The relevant code from Bio/Fasta/__init__.py
>is:
>
>def index_file(filename, indexname, rec2key=None):
>    [...]
>    index[Dictionary._Dictionary__filename_key] = filename
>
>So, if you just pass relative paths, you shouldn't have any problem
>with absolute file names. A solution you could use in your code
>without needing to modify Biopython is to do:
>
>start_dir = os.getcwd()
>os.chdir("whatever/the/directory/is")
>index_file("the_file.fasta", "the_index.idx")
>os.chdir(start_dir)
>
>Then you would have an index with a relative path and you could
>change into this directory later to open the index.
>
>os.chdir("whatever/the/directory/is")
>dict = Fasta.Dictionary("the_index.idx")
>
>  
>
>>For my case, I store fasta_seq_file and its index file at a network 
>>drive and I need to access it from both windows and linux server. The 
>>original index file can not be used for both environments. To solve this 
>>problem, I modified two lines of Bio/Fasta/__init__.py as below. As the 
>>result, it require the index file is placed at the same directory of 
>>fasta_seq_file.
>>    
>>
>[...]
>  
>
>>Do you it's worth to make this modification? Or, any better solution? 
>>    
>>
>
>I'm not a big fan of restricting the index file and fasta file to
>the same directory. A backwards compatible solution would be to
>allow Dictionary to take a filename the index points to as an
>optional argument.
>    
>    def __init__(self, indexname, parser=None, filename = None):
>        self._index = Index.Index(indexname)
>        if filename:
>            self._handle = open(filename)
>        else:
>            self._handle = open(self._index[Dictionary.__filename_key])
>        self._parser = parser
>
>Does this solution seem reasonable? Or will the os.chdir solution
>work for you?
>
>Hope this helps.
>Brad 
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