[BioPython] String instead of file

[Petri Loukasmaki (Genomics)]

On Tue, 11 Sep 2001, Yair Benita wrote:

> Fasta files can be easily parsed like this:
> 
> parser = Fasta.RecordParser()
> iterator = Fasta.Iterator(File.txt, parser)
> cur_record = iterator.next()
> 
> But, how do I parse strings and not a file with this parser?
> I am creating sequences and I want to write the in a Fasta format.
> Simply making a handle does not work, the error is:
> 
> ValueError: I expected a file handle of file-like object

If I remeber correct, the parameter must be a file-interface satisfying
object. With string, this can be archieved by using memoryfiles.
In python, this is implemented by StringIO class, which handles strings as
file-like objects.

So (in theory) following should work:

import StringIO

mystring="a fasta string..."
mystringfile=StringIO.StringIO(mystring)
iterator = Fasta.Iterator(mystringfile, parser)
...

cheers;
------ ----  ---   --   --    --     -      -       -        -
Petri Loukasmäki			petri.loukasmaki@btk.utu.fi
Research Assistant / BioInformatics	tel +358 (0)2 333 8622

Turku Centre for Biotechnology
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