[Biopython-dev] [Bug 2865] Phd writer class for SeqIO

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jul 1 14:39:05 UTC 2009


------- Comment #4 from biopython-bugzilla at maubp.freeserve.co.uk  2009-07-01 10:39 EST -------
(In reply to comment #2)
> Following the email from David Gordon the Consed author via Gordon Roberston
> (thanks Gordon) on the dev list
> (http://lists.open-bio.org/pipermail/biopython-dev/2009-June/006322.html) Ive
> made some changes to the PhdWriter and parser:

Yep - coping with missing peak values sounds like it is required now.

> The writer no longer uses default values for the header COMMENTS (here we
> differ from bioperl).

Do you just leave out the comments? That seems better to me.

> Peak location letter annotations are now optional in both the parsing and
> writing.


> Additional unittest have been added for the examples of 454 and Solexa data
> that David Gordon included in his message.

I'll have to look at those later...

> Note also: Currently we ignore comments in Phd files, ie those beginning with
> "#". Nothing special is done with the version number which is appended to the
> identifier on the BEGIN_SEQUENCE line in phd_ball files.
> Attached is a patch against biopython on github and Ive pushed changes to my
> assembly branch.

I've done another partial merge, still leaving out the writer code. I'm not
going to commit that until next week at the earliest (when I'll be back at
work) as I want to give it a good test first. I'm not sure if this will make it
into Biopython 1.51 final or not. I will however try and add the new example
files and test cases before that.

[Don't feel you have to redo the patch - I can continue to pull bits out of it]

As part of my commit I added a doctest to Bio/SeqIO/PhdIO.py, which has made me
wonder if for SeqIO we should convert the PHRED sequence to upper case (just
because it would look nicer for PHRED to FASTQ conversions).

Thanks again,


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