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GenomeDiagram example Proux_et_al_2002_Figure_6.py needs updating #563

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TheChymera opened this issue Jun 18, 2015 · 5 comments
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GenomeDiagram example Proux_et_al_2002_Figure_6.py needs updating #563

TheChymera opened this issue Jun 18, 2015 · 5 comments

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@TheChymera
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This example file fails with:

Traceback (most recent call last):
  File "test.py", line 127, in <module>
    assert record.name not in feature_sets
AssertionError
@peterjc
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peterjc commented Jun 18, 2015

Are you running the example unmodified? How did you get the sample GenBank files?

@TheChymera
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Yes, unmodified. Got them from the GenBank website.

peterjc added a commit that referenced this issue Jun 18, 2015
@peterjc
Annotation tags have changed in example file.
8457989 
NC_003212 now has new locus_tag entries, the names we
expected are preserved under old_locus_tag.

Something else has changed too... - see also GitHub issue #563.
@peterjc
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peterjc commented Jun 18, 2015

I can't yet explain the error message you have (unless it is a simple mistake like saving a record with the wrong filename?).

Note for NC_003212 via the website you must ask for the FULL record in GenBank format, otherwise you get a summary record with no genes and a CONTIG entry instead of the sequence.

The annotation of this bacteria has been revised and the gene names in this script are now recorded under old_locus_tag. However, even with the locus tag detection tweaked 8457989 , there is something different about the number of features (and thus the colours pre-assigned to them). I suspect something on the annotation has changed subtly...

peterjc added a commit that referenced this issue Jun 18, 2015
@peterjc
Fail gracefully if extra genes present.
537d76b 
Seems revised NC_003212 annotation has another five genes
in the region of interest, so will have to revisit the
manually assigned list of gene colours at some point...

See also GitHub issue #563.
@peterjc peterjc changed the title Broken example code GenomeDiagram example Proux_et_al_2002_Figure_6.py needs updating Dec 17, 2015
@peterjc peterjc mentioned this issue Jul 20, 2017
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@sbliven
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sbliven commented Aug 22, 2017

This should be fixed as of 94c9d7e right?

@peterjc
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peterjc commented Aug 22, 2017

Yep, thank you!

@peterjc peterjc closed this as completed Aug 22, 2017
@peterjc peterjc mentioned this issue Nov 3, 2021
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@peterjc @sbliven @TheChymera