Skip to content

Commit

Permalink
fix allele names for new nomenclature (#248)
Browse files Browse the repository at this point in the history 
* update unit tests to match
  • Loading branch information
@alexlancaster
alexlancaster committed Jan 29, 2025
1 parent a444f39 commit fab4ebf
Show file tree
Hide file tree
Showing 16 changed files with 552 additions and 518 deletions.
8 changes: 4 additions & 4 deletions tests/data/USAFEL-UchiTelle-small.pop
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
labcode method ethnic contin collect latit longit complex
USAFEL 12th Workshop SSOP Telle NW Asia Targen Village 41 deg 12 min N 94 deg 7 min E 1
populat id a_1 a_2 c_1 c_2 b_1 b_2
UchiTelle UT900-23 **** **** 01:02 02:025 **** ****
UchiTelle UT900-23 **** **** 01:02 02:10:06 **** ****
UchiTelle UT900-24 01:01 **** 03:07 06:05 13:01 13:01
UchiTelle UT900-25 02:10 03:012 07:12 01:02 13:01 13:01
UchiTelle UT900-25 02:10 03:01:02 07:12 01:02 13:01 13:01
UchiTelle UT900-26 01:01 02:18 08:04 12:02 13:01 13:01
UchiTelle UT910-01 25:01 02:01 15:07 03:07 13:01 13:01
UchiTelle UT910-02 02:10 32:04 18:01 01:02 13:01 13:01
UchiTelle UT910-03 03:012 32:04 15:07 06:05 13:01 13:01
UchiTelle UT910-03 03:01:02 32:04 15:07 06:05 13:01 13:01
UchiTelle UT910-04 25:01 32:04 03:07 03:07 13:01 13:01
UchiTelle UT910-05 68:14 02:01 01:02 07:12 13:01 13:01
UchiTelle UT922-25 02:01 02:01 12:02 02:025 13:01 13:01
UchiTelle UT922-25 02:01 02:01 12:02 02:10:06 13:01 13:01
6 changes: 3 additions & 3 deletions tests/data/doc-examples/data-hla.pop
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
labcode method ethnic contin collect latit longit
USAFEL 12th Workshop SSOP Telle NW Asia Targen Village 41 deg 12 min N 94 deg 7 min E
populat id a_1 a_2 c_1 c_2 b_1 b_2
UchiTelle UT900-23 **** **** 01:02 02:025 13:01 18:012
UchiTelle UT900-23 **** **** 01:02 02:10:06 13:01 18:012
UchiTelle UT900-24 01:01 02:01 03:07 06:05 14:01 39:021
UchiTelle UT900-25 02:10 03:012 07:12 01:02 15:20 13:01
UchiTelle UT900-25 02:10 03:01:02 07:12 01:02 15:20 13:01
UchiTelle UT900-26 01:01 02:18 08:04 12:02 35:091 40:05
UchiTelle UT910-01 25:01 02:01 15:07 03:07 51:013 14:01
UchiTelle UT910-02 02:10 32:04 18:01 01:02 78:021 13:01
UchiTelle UT910-03 03:012 32:04 15:07 06:05 51:013 39:021
UchiTelle UT910-03 03:01:02 32:04 15:07 06:05 51:013 39:021
6 changes: 3 additions & 3 deletions tests/data/doc-examples/data-minimal-noheader-noids.pop
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
a_1 a_2 c_1 c_2 b_1 b_2
**** **** 01:02 02:025 13:01 18:012
**** **** 01:02 02:10:06 13:01 18:012
01:01 02:01 03:07 06:05 14:01 39:021
02:10 03:012 07:12 01:02 15:20 13:01
02:10 03:01:02 07:12 01:02 15:20 13:01
01:01 02:18 08:04 12:02 35:091 40:05
25:01 02:01 15:07 03:07 51:013 14:01
02:10 32:04 18:01 01:02 78:021 13:01
03:012 32:04 15:07 06:05 51:013 39:021
03:01:02 32:04 15:07 06:05 51:013 39:021
6 changes: 3 additions & 3 deletions tests/data/doc-examples/data-minimal-noheader.pop
View file
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
populat id a_1 a_2 c_1 c_2 b_1 b_2
UchiTelle UT900-23 **** **** 01:02 02:025 13:01 18:012
UchiTelle UT900-23 **** **** 01:02 02:10:06 13:01 18:012
UchiTelle UT900-24 01:01 02:01 03:07 06:05 14:01 39:021
UchiTelle UT900-25 02:10 03:012 07:12 01:02 15:20 13:01
UchiTelle UT900-25 02:10 03:01:02 07:12 01:02 15:20 13:01
UchiTelle UT900-26 01:01 02:18 08:04 12:02 35:091 40:05
UchiTelle UT910-01 25:01 02:01 15:07 03:07 51:013 14:01
UchiTelle UT910-02 02:10 32:04 18:01 01:02 78:021 13:01
UchiTelle UT910-03 03:012 32:04 15:07 06:05 51:013 39:021
UchiTelle UT910-03 03:01:02 32:04 15:07 06:05 51:013 39:021
44 changes: 22 additions & 22 deletions tests/data/gold-output/USAFEL-UchiTelle-small-Filters_CustomBinning-out.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,34 +106,34 @@ Sample Size (n): 10.0
Allele Count (2n): 20
Distinct alleles (k): 9

Counts ordered by frequen| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:025 0.10000 2
02:025 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20
Counts ordered by frequency| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:10:06 0.10000 2
02:10:06 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20


2.2. HardyWeinberg [C]
----------------------
Table of genotypes, format of each cell is: observed/expected.

01:02 0/0.4
02:025 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
01:02 0/0.4
02:10:06 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:0202:10:06 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]

Observed Expected Chi-square DoF p-value
Expand Down
84 changes: 42 additions & 42 deletions ...s/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson-no-slatkin.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,32 +46,32 @@ Sample Size (n): 8.0
Allele Count (2n): 16
Distinct alleles (k): 8

Counts ordered by frequen| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
02:01 0.25000 4 | 01:01 0.06250 1
32:04 0.18750 3 | 02:01 0.25000 4
02:10 0.12500 2 | 02:10 0.12500 2
03:012 0.12500 2 | 02:18 0.06250 1
25:01 0.12500 2 | 03:012 0.12500 2
01:01 0.06250 1 | 25:01 0.12500 2
02:18 0.06250 1 | 32:04 0.18750 3
68:14 0.06250 1 | 68:14 0.06250 1
Total 1.00000 16 | Total 1.00000 16
Counts ordered by frequency| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
02:01 0.25000 4 | 01:01 0.06250 1
32:04 0.18750 3 | 02:01 0.25000 4
02:10 0.12500 2 | 02:10 0.12500 2
03:01:02 0.12500 2 | 02:18 0.06250 1
25:01 0.12500 2 | 03:01:02 0.12500 2
01:01 0.06250 1 | 25:01 0.12500 2
02:18 0.06250 1 | 32:04 0.18750 3
68:14 0.06250 1 | 68:14 0.06250 1
Total 1.00000 16 | Total 1.00000 16


1.2. HardyWeinberg [A]
----------------------
Table of genotypes, format of each cell is: observed/expected.

01:01 0/3e-2
02:01 0/0.2 1/0.5
02:10 0/0.1 0/0.5 0/0.1
02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
01:01 0/3e-2
02:01 0/0.2 1/0.5
02:10 0/0.1 0/0.5 0/0.1
02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
03:01:02 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
01:01 02:01 02:10 02:1803:01:02 25:01 32:04 68:14
[Cols: 1 to 8]

Observed Expected Chi-square DoF p-value
Expand Down Expand Up @@ -106,34 +106,34 @@ Sample Size (n): 10.0
Allele Count (2n): 20
Distinct alleles (k): 9

Counts ordered by frequen| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:025 0.10000 2
02:025 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20
Counts ordered by frequency| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:10:06 0.10000 2
02:10:06 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20


2.2. HardyWeinberg [C]
----------------------
Table of genotypes, format of each cell is: observed/expected.

01:02 0/0.4
02:025 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
01:02 0/0.4
02:10:06 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:0202:10:06 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]

Observed Expected Chi-square DoF p-value
Expand Down
84 changes: 42 additions & 42 deletions tests/data/gold-output/USAFEL-UchiTelle-small-out-no-emhaplofreq-noguothompson.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -46,32 +46,32 @@ Sample Size (n): 8.0
Allele Count (2n): 16
Distinct alleles (k): 8

Counts ordered by frequen| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
02:01 0.25000 4 | 01:01 0.06250 1
32:04 0.18750 3 | 02:01 0.25000 4
02:10 0.12500 2 | 02:10 0.12500 2
03:012 0.12500 2 | 02:18 0.06250 1
25:01 0.12500 2 | 03:012 0.12500 2
01:01 0.06250 1 | 25:01 0.12500 2
02:18 0.06250 1 | 32:04 0.18750 3
68:14 0.06250 1 | 68:14 0.06250 1
Total 1.00000 16 | Total 1.00000 16
Counts ordered by frequency| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
02:01 0.25000 4 | 01:01 0.06250 1
32:04 0.18750 3 | 02:01 0.25000 4
02:10 0.12500 2 | 02:10 0.12500 2
03:01:02 0.12500 2 | 02:18 0.06250 1
25:01 0.12500 2 | 03:01:02 0.12500 2
01:01 0.06250 1 | 25:01 0.12500 2
02:18 0.06250 1 | 32:04 0.18750 3
68:14 0.06250 1 | 68:14 0.06250 1
Total 1.00000 16 | Total 1.00000 16


1.2. HardyWeinberg [A]
----------------------
Table of genotypes, format of each cell is: observed/expected.

01:01 0/3e-2
02:01 0/0.2 1/0.5
02:10 0/0.1 0/0.5 0/0.1
02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
03:012 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
01:01 02:01 02:10 02:18 03:012 25:01 32:04 68:14
01:01 0/3e-2
02:01 0/0.2 1/0.5
02:10 0/0.1 0/0.5 0/0.1
02:18 1/6e-2 0/0.2 0/0.1 0/3e-2
03:01:02 0/0.1 0/0.5 1/0.2 0/0.1 0/0.1
25:01 0/0.1 1/0.5 0/0.2 0/0.1 0/0.2 0/0.1
32:04 0/0.2 0/0.8 1/0.4 0/0.2 1/0.4 1/0.4 0/0.3
68:14 0/6e-2 1/0.2 0/0.1 0/6e-2 0/0.1 0/0.1 0/0.2 0/3e-2
01:01 02:01 02:10 02:1803:01:02 25:01 32:04 68:14
[Cols: 1 to 8]

Observed Expected Chi-square DoF p-value
Expand Down Expand Up @@ -111,34 +111,34 @@ Sample Size (n): 10.0
Allele Count (2n): 20
Distinct alleles (k): 9

Counts ordered by frequen| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:025 0.10000 2
02:025 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20
Counts ordered by frequency| Counts ordered by name
Name Frequency (Count) | Name Frequency (Count)
01:02 0.20000 4 | 01:02 0.20000 4
03:07 0.20000 4 | 02:10:06 0.10000 2
02:10:06 0.10000 2 | 03:07 0.20000 4
06:05 0.10000 2 | 06:05 0.10000 2
07:12 0.10000 2 | 07:12 0.10000 2
12:02 0.10000 2 | 08:04 0.05000 1
15:07 0.10000 2 | 12:02 0.10000 2
08:04 0.05000 1 | 15:07 0.10000 2
18:01 0.05000 1 | 18:01 0.05000 1
Total 1.00000 20 | Total 1.00000 20


2.2. HardyWeinberg [C]
----------------------
Table of genotypes, format of each cell is: observed/expected.

01:02 0/0.4
02:025 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:02 02:025 03:07 06:05 07:12 08:04 12:02 15:07 18:01
01:02 0/0.4
02:10:06 1/0.4 0/0.1
03:07 0/0.8 0/0.4 1/0.4
06:05 0/0.4 0/0.2 1/0.4 0/0.1
07:12 2/0.4 0/0.2 0/0.4 0/0.2 0/0.1
08:04 0/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/3e-2
12:02 0/0.4 1/0.2 0/0.4 0/0.2 0/0.2 1/0.1 0/0.1
15:07 0/0.4 0/0.2 1/0.4 1/0.2 0/0.2 0/0.1 0/0.2 0/0.1
18:01 1/0.2 0/0.1 0/0.2 0/0.1 0/0.1 0/5e-2 0/0.1 0/0.1 0/3e-2
01:0202:10:06 03:07 06:05 07:12 08:04 12:02 15:07 18:01
[Cols: 1 to 9]

Observed Expected Chi-square DoF p-value
Expand Down
Loading

0 comments on commit fab4ebf

Please sign in to comment.