Skip to content

Commit 7d51020

Browse files
nicklomannickloman
authored
Merge pull request #3 from will-rowe/master
adding SARS-CoV-2 schemes and adding latest scheme format to all versions
2 parents ab48f8b + c80c362 commit 7d51020

27 files changed

+9763
-0
lines changed

‎.travis.yml‎

Lines changed: 26 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,26 @@
1+
dist: xenial
2+
language: python # this works for Linux but is an error on macOS or Windows
3+
jobs:
4+
include:
5+
- name: "Python 3.6 on Xenial Linux"
6+
python: 3.6 # this works for Linux but is ignored on macOS or Windows
7+
- name: "Python 3.6 on macOS"
8+
os: osx
9+
language: shell # 'language: python' is an error on Travis CI macOS
10+
python: 3.6
11+
12+
install:
13+
- if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then MINICONDA_OS=Linux; else MINICONDA_OS=MacOSX; fi
14+
- wget https://repo.anaconda.com/miniconda/Miniconda3-latest-$MINICONDA_OS-x86_64.sh -O miniconda.sh
15+
- bash miniconda.sh -b -p "$HOME"/miniconda
16+
- source "$HOME/miniconda/etc/profile.d/conda.sh"
17+
- hash -r
18+
- conda config --set always_yes yes --set changeps1 no
19+
- conda update -q conda
20+
- conda info -a
21+
- conda create -y -n primerSchemes -c conda-forge -c bioconda artic-tools
22+
- conda activate primerSchemes
23+
24+
script:
25+
# validate the schemes using artic-tools
26+
for i in */V*/*.primer.bed; do artic-tools validate_scheme $i; done;

‎LICENSE‎

Lines changed: 21 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,21 @@
1+
MIT License
2+
3+
Copyright (c) 2020 ARTIC Network
4+
5+
Permission is hereby granted, free of charge, to any person obtaining a copy
6+
of this software and associated documentation files (the "Software"), to deal
7+
in the Software without restriction, including without limitation the rights
8+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9+
copies of the Software, and to permit persons to whom the Software is
10+
furnished to do so, subject to the following conditions:
11+
12+
The above copyright notice and this permission notice shall be included in all
13+
copies or substantial portions of the Software.
14+
15+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21+
SOFTWARE.

‎Nipah/V1/NiV_6_Malaysia.primer.bed‎

Lines changed: 120 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,120 @@
1+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1 27 NiV_6_Malaysia_1_LEFT 1 +
2+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 378 401 NiV_6_Malaysia_1_RIGHT 1 -
3+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 319 341 NiV_6_Malaysia_2_LEFT 2 +
4+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 702 726 NiV_6_Malaysia_2_RIGHT 2 -
5+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 640 662 NiV_6_Malaysia_3_LEFT 1 +
6+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1004 1028 NiV_6_Malaysia_3_RIGHT 1 -
7+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 943 965 NiV_6_Malaysia_4_LEFT 2 +
8+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1308 1330 NiV_6_Malaysia_4_RIGHT 2 -
9+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1239 1263 NiV_6_Malaysia_5_LEFT 1 +
10+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1617 1639 NiV_6_Malaysia_5_RIGHT 1 -
11+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1545 1567 NiV_6_Malaysia_6_LEFT 2 +
12+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1900 1929 NiV_6_Malaysia_6_RIGHT 2 -
13+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 1840 1862 NiV_6_Malaysia_7_LEFT 1 +
14+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2212 2234 NiV_6_Malaysia_7_RIGHT 1 -
15+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2179 2204 NiV_6_Malaysia_8_LEFT 2 +
16+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2538 2560 NiV_6_Malaysia_8_RIGHT 2 -
17+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2477 2501 NiV_6_Malaysia_9_LEFT 1 +
18+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2831 2857 NiV_6_Malaysia_9_RIGHT 1 -
19+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 2798 2820 NiV_6_Malaysia_10_LEFT 2 +
20+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3156 3179 NiV_6_Malaysia_10_RIGHT 2 -
21+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3113 3138 NiV_6_Malaysia_11_LEFT 1 +
22+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3471 3493 NiV_6_Malaysia_11_RIGHT 1 -
23+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3435 3457 NiV_6_Malaysia_12_LEFT 2 +
24+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3795 3817 NiV_6_Malaysia_12_RIGHT 2 -
25+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 3718 3740 NiV_6_Malaysia_13_LEFT 1 +
26+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4089 4111 NiV_6_Malaysia_13_RIGHT 1 -
27+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4008 4037 NiV_6_Malaysia_14_LEFT 2 +
28+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4364 4388 NiV_6_Malaysia_14_RIGHT 2 -
29+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4283 4305 NiV_6_Malaysia_15_LEFT 1 +
30+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4652 4674 NiV_6_Malaysia_15_RIGHT 1 -
31+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4571 4596 NiV_6_Malaysia_16_LEFT 2 +
32+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4924 4951 NiV_6_Malaysia_16_RIGHT 2 -
33+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 4878 4907 NiV_6_Malaysia_17_LEFT 1 +
34+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5246 5269 NiV_6_Malaysia_17_RIGHT 1 -
35+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5175 5197 NiV_6_Malaysia_18_LEFT 2 +
36+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5567 5589 NiV_6_Malaysia_18_RIGHT 2 -
37+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5500 5522 NiV_6_Malaysia_19_LEFT 1 +
38+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5873 5901 NiV_6_Malaysia_19_RIGHT 1 -
39+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 5792 5814 NiV_6_Malaysia_20_LEFT 2 +
40+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6145 6172 NiV_6_Malaysia_20_RIGHT 2 -
41+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6081 6103 NiV_6_Malaysia_21_LEFT 1 +
42+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6462 6487 NiV_6_Malaysia_21_RIGHT 1 -
43+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6403 6429 NiV_6_Malaysia_22_LEFT 2 +
44+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6760 6785 NiV_6_Malaysia_22_RIGHT 2 -
45+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 6711 6733 NiV_6_Malaysia_23_LEFT 1 +
46+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7072 7097 NiV_6_Malaysia_23_RIGHT 1 -
47+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7026 7048 NiV_6_Malaysia_24_LEFT 2 +
48+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7385 7409 NiV_6_Malaysia_24_RIGHT 2 -
49+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7346 7368 NiV_6_Malaysia_25_LEFT 1 +
50+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7708 7733 NiV_6_Malaysia_25_RIGHT 1 -
51+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7660 7682 NiV_6_Malaysia_26_LEFT 2 +
52+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8027 8052 NiV_6_Malaysia_26_RIGHT 2 -
53+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 7932 7956 NiV_6_Malaysia_27_LEFT 1 +
54+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8284 8312 NiV_6_Malaysia_27_RIGHT 1 -
55+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8244 8267 NiV_6_Malaysia_28_LEFT 2 +
56+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8604 8632 NiV_6_Malaysia_28_RIGHT 2 -
57+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8503 8526 NiV_6_Malaysia_29_LEFT 1 +
58+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8869 8893 NiV_6_Malaysia_29_RIGHT 1 -
59+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 8821 8850 NiV_6_Malaysia_30_LEFT 2 +
60+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9191 9213 NiV_6_Malaysia_30_RIGHT 2 -
61+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9150 9178 NiV_6_Malaysia_31_LEFT 1 +
62+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9506 9531 NiV_6_Malaysia_31_RIGHT 1 -
63+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9460 9482 NiV_6_Malaysia_32_LEFT 2 +
64+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9829 9851 NiV_6_Malaysia_32_RIGHT 2 -
65+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 9751 9773 NiV_6_Malaysia_33_LEFT 1 +
66+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10124 10148 NiV_6_Malaysia_33_RIGHT 1 -
67+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10075 10100 NiV_6_Malaysia_34_LEFT 2 +
68+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10441 10463 NiV_6_Malaysia_34_RIGHT 2 -
69+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10384 10408 NiV_6_Malaysia_35_LEFT 1 +
70+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10735 10764 NiV_6_Malaysia_35_RIGHT 1 -
71+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10671 10698 NiV_6_Malaysia_36_LEFT 2 +
72+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11029 11052 NiV_6_Malaysia_36_RIGHT 2 -
73+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 10940 10965 NiV_6_Malaysia_37_LEFT 1 +
74+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11308 11333 NiV_6_Malaysia_37_RIGHT 1 -
75+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11261 11283 NiV_6_Malaysia_38_LEFT 2 +
76+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11614 11644 NiV_6_Malaysia_38_RIGHT 2 -
77+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11525 11550 NiV_6_Malaysia_39_LEFT 1 +
78+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11881 11910 NiV_6_Malaysia_39_RIGHT 1 -
79+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 11788 11813 NiV_6_Malaysia_40_LEFT 2 +
80+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12151 12175 NiV_6_Malaysia_40_RIGHT 2 -
81+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12097 12123 NiV_6_Malaysia_41_LEFT 1 +
82+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12469 12494 NiV_6_Malaysia_41_RIGHT 1 -
83+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12378 12403 NiV_6_Malaysia_42_LEFT 2 +
84+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12749 12773 NiV_6_Malaysia_42_RIGHT 2 -
85+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 12712 12737 NiV_6_Malaysia_43_LEFT 1 +
86+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13074 13097 NiV_6_Malaysia_43_RIGHT 1 -
87+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13029 13053 NiV_6_Malaysia_44_LEFT 2 +
88+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13384 13409 NiV_6_Malaysia_44_RIGHT 2 -
89+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13346 13368 NiV_6_Malaysia_45_LEFT 1 +
90+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13704 13726 NiV_6_Malaysia_45_RIGHT 1 -
91+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13670 13694 NiV_6_Malaysia_46_LEFT 2 +
92+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14028 14051 NiV_6_Malaysia_46_RIGHT 2 -
93+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 13968 13990 NiV_6_Malaysia_47_LEFT 1 +
94+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14325 14348 NiV_6_Malaysia_47_RIGHT 1 -
95+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14279 14304 NiV_6_Malaysia_48_LEFT 2 +
96+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14651 14673 NiV_6_Malaysia_48_RIGHT 2 -
97+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14595 14617 NiV_6_Malaysia_49_LEFT 1 +
98+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14946 14976 NiV_6_Malaysia_49_RIGHT 1 -
99+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 14864 14888 NiV_6_Malaysia_50_LEFT 2 +
100+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15228 15253 NiV_6_Malaysia_50_RIGHT 2 -
101+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15148 15171 NiV_6_Malaysia_51_LEFT 1 +
102+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15534 15562 NiV_6_Malaysia_51_RIGHT 1 -
103+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15484 15506 NiV_6_Malaysia_52_LEFT 2 +
104+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15855 15881 NiV_6_Malaysia_52_RIGHT 2 -
105+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 15784 15806 NiV_6_Malaysia_53_LEFT 1 +
106+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16173 16196 NiV_6_Malaysia_53_RIGHT 1 -
107+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16102 16126 NiV_6_Malaysia_54_LEFT 2 +
108+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16455 16483 NiV_6_Malaysia_54_RIGHT 2 -
109+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16403 16433 NiV_6_Malaysia_55_LEFT 1 +
110+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16758 16784 NiV_6_Malaysia_55_RIGHT 1 -
111+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 16709 16733 NiV_6_Malaysia_56_LEFT 2 +
112+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17077 17099 NiV_6_Malaysia_56_RIGHT 2 -
113+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17033 17061 NiV_6_Malaysia_57_LEFT 1 +
114+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17399 17422 NiV_6_Malaysia_57_RIGHT 1 -
115+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17340 17362 NiV_6_Malaysia_58_LEFT 2 +
116+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17701 17726 NiV_6_Malaysia_58_RIGHT 2 -
117+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17669 17691 NiV_6_Malaysia_59_LEFT 1 +
118+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 18025 18049 NiV_6_Malaysia_59_RIGHT 1 -
119+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 17814 17836 NiV_6_Malaysia_60_LEFT 2 +
120+
NiV|AJ564622|NV/MY/99/VRI-1413|pig|Malaysia|||1999 18166 18196 NiV_6_Malaysia_60_RIGHT 2 -

0 commit comments

Comments
 (0)