Hello, I had a quick look at the test suite of python-biopython. Currently, my impression is that most warnings spawning during the test are normal, and more or less related to data or functions being stressed.
The following warning message:
test_lowess ...
/usr/lib/python3/dist-packages/Bio/Statistics/__init__.py:11:
BiopythonDeprecationWarning: Bio.Statistics has been deprecated, and we intend
to remove it in a future release of Biopython.
is caused by:
>>> from Bio.Statistics.lowess import lowess
which is the (deprecated) module being tested.
The following warning:
test_SeqIO_Insdc ...
/build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/GenBank/Scanner.py:304:
BiopythonParserWarning: Non-standard feature line wrapping (didn't break on
comma)?
originates from the test data, looking non-standardly formatted
on purpose:
FT CDS join(1..100,101..110
FT )
FT /protein_id="Test"
FT /db_xref="PEDANT:PE04150000123"
This variant does not complain, but might miss the point of the
test as well (upstream measures tests coverage):
FT CDS join(1..100,101..110)
FT /protein_id="Test"
FT /db_xref="PEDANT:PE04150000123"
Similarly, the next few messages mainly seem caused by the
nature of test data:
test_codonalign ...
/build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/Seq.py:2713:
BiopythonWarning: This table contains 6 codon(s) which code(s) for both STOP
and an amino acid (e.g. 'TAA' -> 'stop' or STOP). Such codons will be
translated as amino acid.
test_PDB_StructureAlignment ...
/build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89:
PDBConstructionWarning: WARNING: Chain A is discontinuous at line 13298.
warnings.warn(
/build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Bio/PDB/StructureBuilder.py:89:
PDBConstructionWarning: WARNING: Chain B is discontinuous at line 13344.
The test against NCBI BLAST tools might be more concerning, the
following warning is outputted several times in a row:
test_NCBI_BLAST_tools ...
/build/python-biopython-1.77+dfsg/.pybuild/cpython3_3.8/build/Tests/test_NCBI_BLAST_tools.py:481:
UserWarning: NCBI BLAST+ blastn and Biopython out sync. Please update
Biopython, or report this issue if you are already using the latest version.
(Extra args: ; Missing:
-negative_taxidlist,-negative_taxids,-sorthits,-sorthsps,-subject_besthit,-taxidlist,-taxids)
But this seems more or less related to this github issue:
https://github.com/biopython/biopython/issues/2184
It is curious as it occurs with makeblastdb 2.10.0, but maybe I
understood the issue the other way around.
Kind Regards,
--
Étienne Mollier <[email protected]>
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