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kylebittinger / brocc

Consensus taxonomy assignment for short reads (great for fungi)
GNU General Public License v3.0
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Test failures after removing GI numbers #4

Open kylebittinger opened 8 years ago

kylebittinger commented 8 years ago

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.

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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)