Package list python-pauvre / 487352f
enabled synplot testing duplicating test data into debian/ for the moment, as they are hosted in another repository. Etienne Mollier 1 year, 7 months ago
9 changed file(s) with 124 addition(s) and 5 deletion(s). Raw diff Collapse all Expand all
55 sh run-unit-test
66
77 in order to confirm its integrity.
8
9
10 Build time tests
11 ────────────────
12
13 Test data are not readily available in upstream repository, but can be
14 retrieved from another repository, from the same author, seemingly dedicated to
15 test data:
16
17 https://github.com/conchoecia/beroe_forskalii_mitogenome/tree/master/gff_files
18
19 Those are made available inside debian/tests/gff_files.
00 #! /bin/bash
11 # pauvre reimplementation in shell: the test suite expects its availability in
2 # the PATH. Appropriate python environment is expected to be set in d/rules.
2 # the PATH.
33 set -ex
4 exec python3 "$CURDIR/pauvre/pauvre_main.py" "$@"
4 export PYTHONPATH="$BUILDDIR"
5 exec python3 "$BUILDDIR/pauvre/pauvre_main.py" "$@"
2121
2222 override_dh_auto_test:
2323 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
24 CURDIR="$(CURDIR)" \
25 PATH="$(CURDIR)/debian/bin:$$PATH" \
26 PYTHONPATH="$(CURDIR)" \
24 PYBUILDDIR="$$(echo "$(CURDIR)"/.pybuild/cpython3_3.*/build)" \
25 && mkdir -p "$${PYBUILDDIR}/pauvre/tests/testdata/alignments" \
26 "$${PYBUILDDIR}/pauvre/tests/testresults" \
27 && cp -r "$(CURDIR)/debian/tests/gff_files" \
28 "$${PYBUILDDIR}/pauvre/tests/testdata" \
29 && BUILDDIR="$${PYBUILDDIR}" PATH="$(CURDIR)/debian/bin:$$PATH" \
2730 dh_auto_test
2831 endif
0 ##gff-version 3
1 ##source-version geneious 9.0.2
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
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
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
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
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