[BioPython] suggestion on Fasta.index_file()

[Brad Chapman]

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