Also fixed two cases of PEP8 spacing.
instead to use hasattr to test the attribute matrix_id I use the block try ... except
When there is content in an EMBL file after SQ or CO lines that is not // or whitespace, the parser throws an AssertionError. Unfortunately, the error message is less than helpful. Improve the error message. This fixes issue #431 Signed-off-by: Kai Blin <firstname.lastname@example.org>
…ull descriptions Previously, the hit description in the hit table always overwrites the full description. This doesn't matter when they are the same, but the description in the tables has a maximum length. If the full description exceeds the length, a truncated version is shown in the table. This change ensures that the full description is always used.
Signed-off-by: Kai Blin <email@example.com>
If the FeatureLocation is None, instead of creating a somewhat obscure AttributeError, explicitly fail with a ValueError. This fixes issue #584 Signed-off-by: Kai Blin <firstname.lastname@example.org>
…coordinates To make sure we notice if we ever change the behaviour discussed in issue #584, explicitly test for this. Signed-off-by: Kai Blin <email@example.com>
See GitHub issue #570, complement(join(...)) as used by NCBI worked, but join(complement(...),complement(...),...) as used by EMBL/ENSEMBL did not. Mention this and recent CompoundLocation reverse complement bug fix in the NEWS file.
…,...)) See GitHub issue #570, seems this wasn't covered by a unit test. Test added to test_SeqIO_features.py using existing template approach.
This was discovered while working on GitHub issue #570.
This reveals a subtle bug in the CompoundLocation._flip(...) method wrongly reversing the order of the parts. Since they are listed in biological order, changing our frame of reference to the other strand coordindates should not change this.
…ersity of British Columbia