[Biopython-dev] [Bug 2454] Iterators can't use file-like objects

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Jul 16 16:08:38 UTC 2008


------- Comment #27 from biopython-bugzilla at maubp.freeserve.co.uk  2008-07-16 12:08 EST -------
Regarding the Bio.Sequencing.Ace changes (comment 26), some of it looks a bit
repetitive.  Might a sub-function help here?  Also, I was wondering if you
managed to fix Bug 2446 as a nice bonus.

Regarding the Bio.Sequencing.Phd changes, Michiel has now deprecated Frank &
Cymon's original scanner/consumer parser.  I didn't think it make sense to
leave the original header as it was (with their old version number etc and the
suggestion to contacting them directly with bugs).  They are of course still
listed in the copyright header.

New Bio.Sequencing.Phd docstring header text in CVS:

Parser for PHD files output by PHRED and used by PHRAP and CONSED.

This module can be used used directly which will return Record objects
which should contain all the original data in the file.

Alternatively, using Bio.SeqIO with the "phd" format will call this module
internally.  This will give SeqRecord objects for each contig sequence.

Previous text:

Parser for PHD files output by PHRED and used by PHRAP and CONSED.

Works fine with PHRED 0.020425.c

Version 1.1, 03/09/2004
written by Cymon J. Cox (cymon.cox at gmail.com ) and
Frank Kauff (fkauff 'AT' biologie.uni-kl.de).
Comments, bugs, problems, suggestions to one of us are welcome!

Frank & Cymon - I should have asked first, but is this revised wording OK with

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