Source: python-bcbio-gff Version: 0.7.1-2 Severity: normal X-Debbugs-Cc: Étienne Mollier <[email protected]>
Hi, The autopkgtest succeeds where it should fail. https://salsa.debian.org/med-team/python-bcbio-gff/-/jobs/9180808 Read in GFF2 and write out as GFF3. ... ok t_gff3_to_gff3 (__main__.OutputTest.t_gff3_to_gff3) Read in and write out GFF3 without any loss of information. ... ok t_write_fasta (__main__.OutputTest.t_write_fasta) Include FASTA records in GFF output. ... ERROR t_write_from_recs (__main__.OutputTest.t_write_from_recs) Write out GFF3 from SeqRecord inputs. ... ERROR t_write_seqrecord (__main__.OutputTest.t_write_seqrecord) Write single SeqRecords. ... ERROR ====================================================================== ERROR: t_basic_solid_parse (__main__.SolidGFFTester.t_basic_solid_parse) Basic parsing of SOLiD GFF results files. ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 381, in t_basic_solid_parse assert test_feature.location.nofuzzy_start == 102716 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start' ====================================================================== ERROR: t_jgi_gff (__main__.GFF2Tester.t_jgi_gff) Parsing of JGI formatted GFF2, nested using transcriptId and proteinID ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 480, in t_jgi_gff assert tfeature.location.nofuzzy_start == 37060 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start' ====================================================================== ERROR: t_write_fasta (__main__.OutputTest.t_write_fasta) Include FASTA records in GFF output. ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 656, in t_write_fasta rec.features = [SeqFeature(FeatureLocation(0, 20), type="gene", strand=1, ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ qualifiers=qualifiers)] ^^^^^^^^^^^^^^^^^^^^^^ TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand' ====================================================================== ERROR: t_write_from_recs (__main__.OutputTest.t_write_from_recs) Write out GFF3 from SeqRecord inputs. ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 630, in t_write_from_recs top_feature = SeqFeature(FeatureLocation(0, 20), type="gene", strand=1, qualifiers=qualifiers) TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand' ====================================================================== ERROR: t_write_seqrecord (__main__.OutputTest.t_write_seqrecord) Write single SeqRecords. ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/autopkgtest-lxc.pswqzcyp/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", line 673, in t_write_seqrecord rec.features = [SeqFeature(FeatureLocation(0, 20), type="gene", strand=1, ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ qualifiers=qualifiers)] ^^^^^^^^^^^^^^^^^^^^^^ TypeError: SeqFeature.__init__() got an unexpected keyword argument 'strand' ---------------------------------------------------------------------- Ran 40 tests in 0.096s FAILED (errors=5) autopkgtest [11:15:46]: test run-unit-test: -----------------------] autopkgtest [11:15:46]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - run-unit-test PASS autopkgtest [11:15:46]: test autodep8-python3: preparing testbed autopkgtest [11:15:56]: testbed dpkg architecture: amd64 autopkgtest [11:15:56]: testbed apt version: 3.1.16
