[Biopython-dev] [Bug 2520] Reading ACE assembly contig files in Bio.SeqIO

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http://bugzilla.open-bio.org/show_bug.cgi?id=2520





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2008-06-17 07:29 EST -------
Created an attachment (id=944)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=944&action=view)
New file Bio/SeqIO/AceIO.py

This new file would be added to Bio.SeqIO in the usual way (updating
Bio/SeqIO/__init__.py to import this module and map the format "ace" to the new
iterator).

Handling different gap characters in Bio.SeqIO (and translating them when
reading and writing files) has not been formalised.  Where possible, converting
them into dashes on loading seems to be a sensisble route to take.

Therefore I deliberately map any "*" gap characters in the consensus sequence
into "-" characters, which are used by default in the alphabet class and are
far more commonly used.  The "*" character is typically associated with a stop
codon in protein sequences, which is another reason to avoid using it here.


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