Tests are slow after removing GI numbers, and we have a few failures, probably due to changes in the NCBI taxonomy. This will have to be addressed before the remove-gi-numbers branch is merged.
Test failures:
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FAIL: test_chris_combo95 (__main__.BroccAcceptance)
Representative sequences from Hoffmann COMBO fungi paper.
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Traceback (most recent call last):
File "tests/test_brocc.py", line 93, in test_chris_combo95
read_from(data_fp("chris_combo95_assignments.txt")))
AssertionError: Lists differ: ['0 C.3053_187446\tEukaryota;F... != ['0 C.3053_187446\tEukaryota;F...
First differing element 279:
35 C.4025_819372 Eukaryota;Fungi
35 C.4025_819372 Eukaryota;Fungi;uncultured fungus (phylum)
Diff is 41673 characters long. Set self.maxDiff to None to see it.
======================================================================
FAIL: test_mouseabx_120k (__main__.BroccAcceptance)
All unique fungal reads from Dollive mouse abx paper.
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Traceback (most recent call last):
File "tests/test_brocc.py", line 86, in test_mouseabx_120k
read_from(data_fp("mouseabx_120k_assignments.txt")))
AssertionError: Lists differ: ['0 Af.28.A4_43516\tEukaryota;... != ['0 Af.28.A4_43516\tEukaryota;...
First differing element 0:
0 Af.28.A4_43516 Eukaryota;Fungi;Ascomycota;Eurotiomycetes;Eurotiales;Trichocomaceae;Thermomyces;Thermomyces lanuginosus
0 Af.28.A4_43516 Eukaryota;Fungi;Ascomycota;Eurotiomycetes;Eurotiales;Eurotiales sp. AP-2012 (family);Eurotiales sp. AP-2012 (genus);Eurotiales sp. AP-2012
Diff is 2248191 characters long. Set self.maxDiff to None to see it.
======================================================================
FAIL: test_serena_controls (__main__.BroccAcceptance)
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Traceback (most recent call last):
File "tests/test_brocc.py", line 79, in test_serena_controls
read_from(data_fp("serena_controls_assignments.txt")))
AssertionError: Lists differ: ['0 Candida.glabrata_157\tEuka... != ['0 Candida.glabrata_157\tEuka...
First differing element 4:
12 Plasmodium.falciparum.7G8_822 Eukaryota;Fungi;Ascomycota;Saccharomycetes;Saccharomycetales
12 Plasmodium.falciparum.7G8_822 Eukaryota;Fungi;Ascomycota;Saccharomycetes;Saccharomycetales;Phaffomycetaceae;Cyberlindnera
Diff is 5181 characters long. Set self.maxDiff to None to see it.
----------------------------------------------------------------------
Ran 8 tests in 44807.115s
FAILED (failures=3)
Tests are slow after removing GI numbers, and we have a few failures, probably due to changes in the NCBI taxonomy. This will have to be addressed before the remove-gi-numbers branch is merged.
Test failures: