[Biopython-dev] [Bug 3000] Could SeqIO.parse() store the whole, unparsed multiline entry?

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3000


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #5 from biopython-bugzilla at maubp.freeserve.co.uk  2010-04-02 08:38 EST -------
(In reply to comment #3)
> Created an attachment (id=1436)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=1436&action=view) [details]
> Adds a get_raw method to the dictionaries returned by Bio.SeqIO.index()
> 
> Outline implementation of an alternative proposal, allowing access to the
> raw text for each record via the Bio.SeqIO.index() dictionary like objects.
> See discussion here:
> http://lists.open-bio.org/pipermail/biopython-dev/2010-February/007301.html

Following a positive discussion on the mailing list, I have just checked in
an updated patch including FASTQ file support, unit tests and documentation.
Right now the only indexed file format not supported by the get_raw method is
SFF... which could be done with a little more more.

Although this does not implement the original request ("Could SeqIO.parse()
store the whole, unparsed multiline entry?"), it does allow the original
use case to be solved neatly with Bio.SeqIO - so I'm marking this bug as fixed.

Peter


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