[Biopython-dev] [Biopython - Bug #3278] SeqIO tries to use Gapped without import

[redmine at redmine.open-bio.org]

Issue #3278 has been updated by Peter Cock.


Looking at Biopython 1.53 (December 2009) you appear to be correct.

However, the function was explicitly made obsolete in Biopython 1.54 (with a deprecation warning), and at that point this error did not exist.

Unless there a related problem in the current release, I will close this report.

Thanks.
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Bug #3278: SeqIO tries to use Gapped without import
https://redmine.open-bio.org/issues/3278

Author: Paul Agapow
Status: New
Priority: Normal
Assignee: Biopython Dev Mailing List
Category: Main Distribution
Target version: 1.53
URL: 


@to_alignment@ in @SeqIO@ uses @Gapped@ (@ isinstance(alphabet, Gapped)@) but does not actually import @Gapped at . Thus a @NameError@ results. Although the method is labelled obsolete, it is used by @SeqIO@ in write when an @AlignIO@ writer must be used (e.g. when trying to write sequences to a Nexus file).

Solution: @from Bio.Alphabet import Gapped@


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