enabled synplot testing
duplicating test data into debian/ for the moment, as they are
hosted in another repository.
Etienne Mollier
3 years ago
| 5 | 5 |
sh run-unit-test
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| 6 | 6 |
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| 7 | 7 |
in order to confirm its integrity.
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Build time tests
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────────────────
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Test data are not readily available in upstream repository, but can be
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retrieved from another repository, from the same author, seemingly dedicated to
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test data:
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https://github.com/conchoecia/beroe_forskalii_mitogenome/tree/master/gff_files
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Those are made available inside debian/tests/gff_files.
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| 0 | 0 |
#! /bin/bash
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| 1 | 1 |
# pauvre reimplementation in shell: the test suite expects its availability in
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| 2 | |
# the PATH. Appropriate python environment is expected to be set in d/rules.
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# the PATH.
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| 3 | 3 |
set -ex
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| 4 | |
exec python3 "$CURDIR/pauvre/pauvre_main.py" "$@"
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export PYTHONPATH="$BUILDDIR"
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exec python3 "$BUILDDIR/pauvre/pauvre_main.py" "$@"
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| 21 | 21 |
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| 22 | 22 |
override_dh_auto_test:
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| 23 | 23 |
ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
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| 24 | |
CURDIR="$(CURDIR)" \
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| 25 | |
PATH="$(CURDIR)/debian/bin:$$PATH" \
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| 26 | |
PYTHONPATH="$(CURDIR)" \
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PYBUILDDIR="$$(echo "$(CURDIR)"/.pybuild/cpython3_3.*/build)" \
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&& mkdir -p "$${PYBUILDDIR}/pauvre/tests/testdata/alignments" \
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"$${PYBUILDDIR}/pauvre/tests/testresults" \
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&& cp -r "$(CURDIR)/debian/tests/gff_files" \
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"$${PYBUILDDIR}/pauvre/tests/testdata" \
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&& BUILDDIR="$${PYBUILDDIR}" PATH="$(CURDIR)/debian/bin:$$PATH" \
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| 27 | 30 |
dh_auto_test
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| 28 | 31 |
endif
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0 |
##gff-version 3
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|
1 |
##source-version geneious 9.0.2
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|
2 |
Bf201706_circ Geneious region 1 13338 . + 0 Is_circular=true
|
|
3 |
Bf201706_circ Geneious rRNA 2256 3115 . + . Name=16S
|
|
4 |
Bf201706_circ Geneious rRNA 1880 2255 . + . Name=12S
|
|
5 |
Bf201706_circ Geneious gene 1 1524 . + . Name=COX1
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|
6 |
Bf201706_circ Geneious gene 5981 7459 . + . Name=ND5
|
|
7 |
Bf201706_circ Geneious gene 4699 5781 . + . Name=ND4
|
|
8 |
Bf201706_circ Geneious gene 7608 8672 . + . Name=URF1
|
|
9 |
Bf201706_circ Geneious gene 10863 11918 . + . Name=CYTB
|
|
10 |
Bf201706_circ Geneious gene 11837 12751 . + . Name=ND1
|
|
11 |
Bf201706_circ Geneious gene 3308 4051 . + . Name=COX3
|
|
12 |
Bf201706_circ Geneious gene 10016 10744 . + . Name=ND2
|
|
13 |
Bf201706_circ Geneious gene 9200 9868 . + . Name=URF2
|
|
14 |
Bf201706_circ Geneious gene 12757 13320 . + . Name=COX2
|
|
15 |
Bf201706_circ Geneious gene 4324 4698 . + . Name=ND3
|
|
16 |
Bf201706_circ Geneious gene 3099 3302 . + . Name=ND6
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|
17 |
Bf201706_circ Geneious gene 5781 5969 . + . Name=ND4L
|
|
0 |
##gff-version 3
|
|
1 |
##source-version geneious 9.0.2
|
|
2 |
JN392469 Geneious region 1 11017 . + 0 Is_circular=true
|
|
3 |
JN392469 Geneious source 1 11017 . + . Name=source Pleurobrachia bachei
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|
4 |
JN392469 Geneious gene 1 1539 . + . Name=COX1 gene
|
|
5 |
JN392469 Geneious gene 1660 2241 . + . Name=COX2 gene
|
|
6 |
JN392469 Geneious rRNA 2518 3460 . + . Name=16S rRNA
|
|
7 |
JN392469 Geneious rRNA 3491 4053 . + . Name=12S rRNA
|
|
8 |
JN392469 Geneious gene 4054 4794 . + . Name=COX3 gene
|
|
9 |
JN392469 Geneious gene 4802 5470 . + . Name=ND2 gene
|
|
10 |
JN392469 Geneious gene 5521 5841 . + . Name=ND3 gene
|
|
11 |
JN392469 Geneious gene 5842 6912 . + . Name=ND4 gene
|
|
12 |
JN392469 Geneious gene 7074 8156 . + . Name=CYTB gene
|
|
13 |
JN392469 Geneious gene 8158 9672 . + . Name=ND5 gene
|
|
14 |
JN392469 Geneious gene 9672 10511 . + . Name=ND1 gene
|
|
15 |
JN392469 Geneious gene 10511 10708 . + . Name=ND6 gene
|
|
16 |
JN392469 Geneious gene 10803 11003 . + . Name=ND4L gene⏎
|
|
0 |
##gff-version 3
|
|
1 |
##source-version geneious 9.0.2
|
|
2 |
LN898113 Geneious region 1 11574 . + 0 Is_circular=true
|
|
3 |
LN898113 Geneious source 1 11574 . + . Name=source Coeloplana loyai
|
|
4 |
LN898113 Geneious gene 1 1551 . + . Name=COX1 gene
|
|
5 |
LN898113 Geneious gene 1556 2131 . + . Name=COX2 gene
|
|
6 |
LN898113 Geneious gene 2136 3242 . + . Name=ND4 gene
|
|
7 |
LN898113 Geneious gene 3242 3982 . + . Name=ND2 gene
|
|
8 |
LN898113 Geneious rRNA 4707 5549 . + . Name=16S rRNA
|
|
9 |
LN898113 Geneious rRNA 5550 5962 . + . Name=12S rRNA
|
|
10 |
LN898113 Geneious gene 5963 6190 . + . Name=ND4L gene
|
|
11 |
LN898113 Geneious gene 6192 7484 . + . Name=ND1 gene
|
|
12 |
LN898113 Geneious gene 7488 8555 . + . Name=CYTB gene
|
|
13 |
LN898113 Geneious gene 8556 9314 . + . Name=COX3 gene
|
|
14 |
LN898113 Geneious gene 9314 9655 . + . Name=ND3 gene
|
|
15 |
LN898113 Geneious gene 9790 11307 . + . Name=ND5 gene
|
|
16 |
LN898113 Geneious gene 11309 11515 . + . Name=ND6 gene
|
|
0 |
##gff-version 3
|
|
1 |
##source-version geneious 9.0.2
|
|
2 |
LN898114 Geneious region 1 11551 . + 0 Is_circular=true
|
|
3 |
LN898114 Geneious source 1 11551 . + . Name=source Coeloplana yulianicorum
|
|
4 |
LN898114 Geneious gene 1 1551 . + . Name=COX1 gene
|
|
5 |
LN898114 Geneious gene 1561 2136 . + . Name=COX2 gene
|
|
6 |
LN898114 Geneious gene 2137 3243 . + . Name=ND4 gene
|
|
7 |
LN898114 Geneious gene 3243 3983 . + . Name=ND2 gene
|
|
8 |
LN898114 Geneious rRNA 4694 5540 . + . Name=16S rRNA
|
|
9 |
LN898114 Geneious rRNA 5541 5948 . + . Name=12S rRNA
|
|
10 |
LN898114 Geneious gene 5949 6221 . + . Name=ND4L gene
|
|
11 |
LN898114 Geneious gene 6235 7482 . + . Name=ND1 gene
|
|
12 |
LN898114 Geneious gene 7488 8555 . + . Name=CYTB gene
|
|
13 |
LN898114 Geneious gene 8556 9314 . + . Name=COX3 gene
|
|
14 |
LN898114 Geneious gene 9314 9655 . + . Name=ND3 gene
|
|
15 |
LN898114 Geneious gene 9785 11302 . + . Name=ND5 gene
|
|
16 |
LN898114 Geneious gene 11304 11510 . + . Name=ND6 gene
|
|
0 |
##gff-version 3
|
|
1 |
##source-version geneious 9.0.2
|
|
2 |
LN898115 Geneious region 1 9961 . + 0 Is_circular=true
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|
3 |
LN898115 Geneious source 1 9961 . + . Name=source Vallicula multiformis
|
|
4 |
LN898115 Geneious gene 1 1533 . + . Name=COX1 gene
|
|
5 |
LN898115 Geneious gene 1523 2080 . + . Name=COX2 gene
|
|
6 |
LN898115 Geneious gene 2074 3126 . + . Name=ND4 gene
|
|
7 |
LN898115 Geneious rRNA 3127 3951 . + . Name=16S rRNA
|
|
8 |
LN898115 Geneious rRNA 3952 4306 . + . Name=12S rRNA
|
|
9 |
LN898115 Geneious gene 4307 5011 . + . Name=ND2 gene
|
|
10 |
LN898115 Geneious gene 5011 6048 . + . Name=CYTB gene
|
|
11 |
LN898115 Geneious gene 6032 6799 . + . Name=COX3 gene
|
|
12 |
LN898115 Geneious gene 6796 7119 . + . Name=ND3 gene
|
|
13 |
LN898115 Geneious gene 7124 8569 . + . Name=ND5 gene
|
|
14 |
LN898115 Geneious gene 8577 8792 . + . Name=ND4L gene
|
|
15 |
LN898115 Geneious gene 8792 9655 . + . Name=ND1 gene
|
|
16 |
LN898115 Geneious CDS 9751 9948 . + . Name=ND6 CDS
|
|
0 |
##gff-version 3
|
|
1 |
##source-version geneious 9.0.2
|
|
2 |
NC_016117 Geneious region 1 10326 . + 0 Is_circular=true
|
|
3 |
NC_016117 Geneious source 1 10326 . + . Name=source Mnemiopsis leidyi
|
|
4 |
NC_016117 Geneious rRNA 3521 4398 . + . Name=16S rRNA
|
|
5 |
NC_016117 Geneious rRNA 3153 3520 . + . Name=12S rRNA
|
|
6 |
NC_016117 Geneious gene 1 1524 . + . Name=COX1 gene
|
|
7 |
NC_016117 Geneious gene 6527 7933 . + . Name=ND5 gene
|
|
8 |
NC_016117 Geneious gene 4399 5493 . + . Name=ND4 gene
|
|
9 |
NC_016117 Geneious gene 8775 9860 . + . Name=CYTB gene
|
|
10 |
NC_016117 Geneious gene 7933 8802 . + . Name=ND1 gene
|
|
11 |
NC_016117 Geneious gene 1525 2250 . + . Name=COX3 gene
|
|
12 |
NC_016117 Geneious gene 5495 6220 . + . Name=ND2 gene
|
|
13 |
NC_016117 Geneious gene 2574 3152 . + . Name=COX2 gene
|
|
14 |
NC_016117 Geneious gene 2247 2573 . + . Name=ND3 gene
|
|
15 |
NC_016117 Geneious gene 9847 10050 . + . Name=ND6 gene
|
|
16 |
NC_016117 Geneious gene 6221 6418 . + . Name=ND4L gene⏎
|