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
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:
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()
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