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

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2865





------- Comment #2 from cymon.cox at gmail.com  2009-07-01 10:12 EST -------
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:

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

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.

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.

Cheers, C.


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