[Biopython-dev] Bio.SeqIO

Peter biopython-dev at maubp.freeserve.co.uk
Sat Feb 24 23:41:36 UTC 2007

Another update on the Bio.SeqIO code...

Based on the previous discussions (e.g. Iddo's well argued emails in 
November 2006) I have now removed the code for mapping known file 
extensions to file formats.

The file format is now a required argument (it can be made into an 
optional argument in future if we decide to support file format guessing 
one day).

The provisional documentation is here, which now includes a few examples 
converting from one file format to another - selecting only certain records:


Are you all happy with the interface defined in Bio/SeqIO/__init__.py 
consisting of the four functions:

SequenceIterator(handle, format)
SequencesToDict(sequences, key_function=None)
SequencesToAlignment(sequences, ...)
WriteSequences(sequences, handle, format)

Does anyone want to suggest different names for these functions?

Do you think the argument order is sensible for WriteSequences?

Note that we may want to improve the generic alignment class at some 
point (e.g. see bug 1944).  If alignments could be initialized from a 
SeqRecord list/iterator this would make the SequencesToAlignment() 
function "obsolete"...


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