Skip to content

Commit

Permalink
add missing test data
Browse files Browse the repository at this point in the history
  • Loading branch information
@nebfield
nebfield committed Oct 8, 2024
1 parent e246ff8 commit f857d79
Show file tree
Hide file tree
Showing 7 changed files with 2,899 additions and 1 deletion.
2 changes: 1 addition & 1 deletion pgscatalog.match/src/pgscatalog/match/lib/targetvariants.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ class TargetVariants:
"""A container of :class:`TargetVariant`
:raises: FileNotFoundError
>>> from pgscatalog.core import Config # ignore, only to load test data
>>> from pgscatalog.match.lib._config import Config # ignore, only to load test data
>>> pvar = TargetVariants(Config.ROOT_DIR / "tests" / "data" / "hapnest.pvar")
>>> pvar.ftype
<TargetType.PVAR: 1>
Expand Down
2,696 changes: 2,696 additions & 0 deletions pgscatalog.match/tests/data/1000G.pvar
View file

Large diffs are not rendered by default.

101 changes: 101 additions & 0 deletions pgscatalog.match/tests/data/hapnest.bim
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,101 @@
1 1:10180:T:C 0 10180 C T
7 7:134656486:T:G 0 134656486 G T
1 1:11721077:C:G 0 11721077 G C
1 1:39613790:C:T 0 39613790 T C
13 13:32082404:A:G 0 32082404 G A
16 16:20257914:A:T 0 20257914 T A
10 10:10819548:T:C 0 10819548 C T
7 7:37179341:G:A 0 37179341 A G
4 4:168408254:A:C 0 168408254 C A
3 3:16083234:G:A 0 16083234 A G
21 21:20501825:A:C 0 20501825 C A
9 9:32533377:T:G 0 32533377 G T
7 7:140305903:A:C 0 140305903 C A
12 12:8809481:T:C 0 8809481 C T
18 18:29102353:G:C 0 29102353 C G
3 3:61104800:T:G 0 61104800 G T
16 16:51841527:C:T 0 51841527 T C
1 1:105182225:C:G 0 105182225 G C
11 11:109920466:G:A 0 109920466 A G
17 17:14748954:T:A 0 14748954 A T
7 7:17258827:T:C 0 17258827 C T
8 8:85512387:G:A 0 85512387 A G
12 12:93820193:C:G 0 93820193 G C
10 10:113809058:A:G 0 113809058 G A
2 2:150276127:A:C 0 150276127 C A
11 11:102399320:T:C 0 102399320 C T
12 12:12057455:G:C 0 12057455 C G
7 7:32080345:C:T 0 32080345 T C
14 14:43694484:A:G 0 43694484 G A
13 13:27849542:G:A 0 27849542 A G
20 20:1244130:A:C 0 1244130 C A
17 17:9144202:G:A 0 9144202 A G
1 1:29317603:C:T 0 29317603 T C
10 10:76920024:A:G 0 76920024 G A
3 3:115883003:T:A 0 115883003 A T
6 6:124852106:C:A 0 124852106 A C
2 2:213405218:A:G 0 213405218 G A
6 6:32665891:A:G 0 32665891 G A
1 1:230071686:C:A 0 230071686 A C
1 1:44981867:G:A 0 44981867 A G
6 6:1172152:T:A 0 1172152 A T
17 17:71511010:G:T 0 71511010 T G
4 4:38361365:G:A 0 38361365 A G
3 3:33800089:C:T 0 33800089 T C
15 15:43642481:T:G 0 43642481 G T
19 19:608415:T:A 0 608415 A T
16 16:7006777:A:G 0 7006777 G A
15 15:64063083:C:G 0 64063083 G C
21 21:29486973:T:A 0 29486973 A T
4 4:118193593:G:A 0 118193593 A G
3 3:69403814:C:T 0 69403814 T C
1 1:153261102:C:T 0 153261102 T C
10 10:9200696:G:T 0 9200696 T G
13 13:26540187:A:C 0 26540187 C A
20 20:61697594:T:C 0 61697594 C T
5 5:112479351:T:C 0 112479351 C T
5 5:135768146:T:G 0 135768146 G T
6 6:95990251:C:T 0 95990251 T C
8 8:31103809:A:G 0 31103809 G A
2 2:235704209:C:T 0 235704209 T C
5 5:85661266:G:T 0 85661266 T G
8 8:108159869:T:C 0 108159869 C T
4 4:125660650:A:G 0 125660650 G A
1 1:24390376:G:C 0 24390376 C G
12 12:105430661:T:G 0 105430661 G T
6 6:97883258:G:A 0 97883258 A G
21 21:10397844:G:A 0 10397844 A G
22 22:22567576:A:G 0 22567576 G A
19 19:35475039:C:T 0 35475039 T C
3 3:122825548:C:T 0 122825548 T C
3 3:178382028:C:T 0 178382028 T C
9 9:17054339:T:C 0 17054339 C T
1 1:200532015:A:G 0 200532015 G A
7 7:52926753:A:C 0 52926753 C A
10 10:74188719:A:C 0 74188719 C A
16 16:77365315:C:T 0 77365315 T C
1 1:187327571:C:T 0 187327571 T C
19 19:1943722:G:A 0 1943722 A G
20 20:46768014:A:G 0 46768014 G A
6 6:32576028:C:A 0 32576028 A C
16 16:49083500:A:C 0 49083500 C A
1 1:162343247:C:A 0 162343247 A C
4 4:187573315:G:T 0 187573315 T G
19 19:28605486:G:A 0 28605486 A G
2 2:136784681:C:G 0 136784681 G C
13 13:113417998:T:C 0 113417998 C T
4 4:161994747:T:C 0 161994747 C T
6 6:112222338:T:C 0 112222338 C T
4 4:172128098:C:T 0 172128098 T C
12 12:11565585:T:C 0 11565585 C T
20 20:4158102:T:G 0 4158102 G T
9 9:120426593:T:G 0 120426593 G T
2 2:398808:A:G 0 398808 G A
4 4:161283226:T:G 0 161283226 G T
5 5:141145283:C:T 0 141145283 T C
1 1:103866518:T:A 0 103866518 A T
5 5:172360827:G:A 0 172360827 A G
1 1:53533836:C:T 0 53533836 T C
8 8:14127525:G:A 0 14127525 A G
7 7:134232094:G:T 0 134232094 T G
8 8:13064579:G:A 0 13064579 A G
Binary file added pgscatalog.match/tests/data/hapnest.bim.gz
View file
Binary file not shown.
Binary file added pgscatalog.match/tests/data/hapnest.bim.zst
View file
Binary file not shown.
101 changes: 101 additions & 0 deletions pgscatalog.match/tests/data/hapnest.pvar
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,101 @@
#CHROM POS ID REF ALT
14 65003549 14:65003549:T:C T C
6 120728654 6:120728654:T:G T G
18 78647111 18:78647111:C:G C G
10 38165112 10:38165112:A:C A C
2 16465434 2:16465434:A:T A T
2 18099452 2:18099452:G:A G A
10 69581826 10:69581826:C:T C T
12 58976609 12:58976609:T:C T C
7 153136231 7:153136231:C:T C T
18 79563047 18:79563047:G:T G T
12 123551234 12:123551234:G:A G A
2 23527532 2:23527532:A:C A C
14 22548407 14:22548407:G:A G A
3 130475609 3:130475609:T:C T C
7 21253009 7:21253009:T:C T C
12 119557448 12:119557448:A:G A G
6 129052159 6:129052159:A:G A G
3 124027392 3:124027392:C:T C T
10 128006754 10:128006754:C:T C T
2 66161158 2:66161158:T:C T C
4 161470095 4:161470095:T:A T A
5 158827062 5:158827062:G:T G T
1 218763451 1:218763451:G:A G A
11 97734128 11:97734128:A:G A G
9 111942320 9:111942320:A:C A C
6 3859464 6:3859464:T:G T G
14 80420391 14:80420391:G:A G A
12 127816132 12:127816132:A:G A G
20 53482880 20:53482880:G:T G T
10 80983233 10:80983233:C:T C T
4 87853953 4:87853953:G:T G T
12 103935434 12:103935434:A:G A G
11 23511590 11:23511590:C:T C T
4 89612378 4:89612378:A:C A C
6 100441665 6:100441665:T:G T G
4 47881746 4:47881746:T:C T C
1 31200416 1:31200416:T:C T C
2 43862280 2:43862280:G:A G A
4 91347364 4:91347364:A:C A C
4 90457528 4:90457528:G:C G C
11 36167289 11:36167289:C:T C T
20 62564230 20:62564230:G:A G A
13 55975591 13:55975591:T:G T G
13 83522866 13:83522866:C:G C G
9 79037973 9:79037973:G:C G C
14 81705439 14:81705439:G:A G A
7 8045500 7:8045500:C:T C T
3 107343500 3:107343500:C:T C T
10 112125687 10:112125687:A:G A G
2 123058409 2:123058409:A:T A T
10 117516178 10:117516178:G:A G A
7 105845171 7:105845171:T:C T C
21 36325044 21:36325044:G:A G A
2 174112570 2:174112570:A:G A G
5 24396997 5:24396997:T:A T A
1 240406092 1:240406092:T:G T G
4 75526249 4:75526249:T:G T G
3 86757425 3:86757425:A:G A G
12 92076522 12:92076522:A:G A G
19 20705155 19:20705155:A:G A G
2 228736479 2:228736479:A:G A G
3 195035182 3:195035182:G:A G A
1 82497197 1:82497197:C:T C T
6 156972653 6:156972653:A:G A G
4 69541781 4:69541781:A:C A C
6 7026712 6:7026712:C:T C T
3 87295732 3:87295732:A:G A G
2 214847124 2:214847124:A:G A G
17 643306 17:643306:G:T G T
10 57635629 10:57635629:A:T A T
17 27238129 17:27238129:G:A G A
7 89172383 7:89172383:T:C T C
15 71654468 15:71654468:C:A C A
8 5303142 8:5303142:A:G A G
20 667181 20:667181:G:A G A
8 130814375 8:130814375:G:A G A
4 78330008 4:78330008:A:G A G
18 62230085 18:62230085:G:T G T
4 83681597 4:83681597:T:G T G
10 4184392 10:4184392:A:C A C
6 3712839 6:3712839:G:T G T
8 129112804 8:129112804:A:C A C
12 2050427 12:2050427:G:T G T
3 126825103 3:126825103:A:G A G
5 117563204 5:117563204:T:C T C
21 8988127 21:8988127:G:T G T
19 27252390 19:27252390:C:T C T
4 40040603 4:40040603:A:C A C
17 42303828 17:42303828:G:T G T
22 11954137 22:11954137:C:T C T
14 19413892 14:19413892:A:C A C
4 130648503 4:130648503:G:A G A
15 73770540 15:73770540:C:A C A
15 101767713 15:101767713:T:C T C
5 82690296 5:82690296:T:G T G
17 58830876 17:58830876:G:A G A
13 85796692 13:85796692:T:C T C
3 44307108 3:44307108:T:C T C
6 100083709 6:100083709:A:G A G
19 23005721 19:23005721:G:A G A
Binary file added pgscatalog.match/tests/data/hapnest.pvar.zst
View file
Binary file not shown.

0 comments on commit f857d79

Please sign in to comment.