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Update docs #81

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4c30773
Update description as a fork
HarryHung Jul 12, 2023
fb65df8
Install specific versions of pysam and pymummer
HarryHung Jul 12, 2023
fccc937
Update Dockerfile based on StaPH-B version
HarryHung Jul 12, 2023
f7f5824
Fix assignment of default values
HarryHung Jul 12, 2023
f52a0d9
Add back cov default value to Serotyping class
HarryHung Jul 13, 2023
e8af62c
Add back clean default value to Serotyping class
HarryHung Jul 13, 2023
e431f0d
Fix pyYAML version issue
HarryHung Jul 13, 2023
a351bbd
Include built-in test in test stage
HarryHung Jul 13, 2023
b0c2f92
Improve README.md as a Docker build
HarryHung Jul 13, 2023
d34d821
Add automated test on PR
HarryHung Jul 13, 2023
48b8406
Merge pull request #1 from HarryHung/feature/github-auto-test
HarryHung Jul 13, 2023
36c15b7
Create docker-image-build-to-test.yml
HarryHung Jul 13, 2023
3299307
Remove non-functional action
HarryHung Jul 13, 2023
87db0ca
Merge pull request #3 from HarryHung/bugfix/build-to-test
HarryHung Jul 13, 2023
36065ba
Merge pull request #4 from HarryHung/bugfix/fixing-seroba
HarryHung Jul 13, 2023
6653557
update db to 1.2.1
Sep 22, 2023
141d418
add yml loader
Sep 22, 2023
502278a
Create GH action for automated deployment
HarryHung Sep 26, 2023
3084506
Merge pull request #1 from HarryHung/feature/automated-deployment
HarryHung Sep 26, 2023
aeaefb8
Correct Docker Image tag
HarryHung Sep 26, 2023
381a5dd
Allow reusing this workflow
HarryHung Sep 26, 2023
9e2fe9a
Build to test before publishing image
HarryHung Sep 26, 2023
d5edfe6
Merge pull request #5 from Oliver-Lorenz-dev/update-db
Oliver-Lorenz-dev Sep 27, 2023
91d351c
Publish to Docker Hub in addition to GitHub Packages
HarryHung Sep 27, 2023
e8903e5
Re-add build-to-test before publish
HarryHung Sep 27, 2023
3ca875f
Fix images publish
HarryHung Sep 27, 2023
352d4f6
Build to app stage only for publish image
HarryHung Sep 28, 2023
5c55df6
Re-adding correct Docker Image tag
HarryHung Sep 28, 2023
59a1221
Merge pull request #6 from HarryHung/master
HarryHung Oct 2, 2023
6a06187
v1.0.4
Oct 2, 2023
142d179
Merge pull request #7 from sanger-bentley-group/update-version
Oliver-Lorenz-dev Oct 2, 2023
7de67f8
update kmc params for newer version
Oliver-Lorenz-dev Oct 11, 2023
f3a082b
updated kmc version
Oliver-Lorenz-dev Oct 11, 2023
fa3a1c5
kmc 3.2.2
Oliver-Lorenz-dev Oct 11, 2023
f3d8ff4
fix typo
Oliver-Lorenz-dev Oct 11, 2023
3c2cbf0
add kmc dir to path
Oliver-Lorenz-dev Oct 11, 2023
dfa2d79
v1.0.5
Oliver-Lorenz-dev Oct 12, 2023
248a0e5
Merge pull request #8 from sanger-bentley-group/upgrade-kmc
Oliver-Lorenz-dev Oct 17, 2023
2560bee
fixes for db
Oliver-Lorenz-dev Feb 28, 2024
a691d4f
add 35B
Oliver-Lorenz-dev Feb 28, 2024
93130ed
1.0.6
Oliver-Lorenz-dev Feb 29, 2024
4028d75
Merge pull request #9 from sanger-bentley-group/fix-db
Oliver-Lorenz-dev Feb 29, 2024
2a93022
rename 10X, 39X and 20
Oliver-Lorenz-dev Mar 4, 2024
f2a0ee4
ignore tmp db files
Oliver-Lorenz-dev Mar 4, 2024
f159541
1.0.7
Oliver-Lorenz-dev Mar 4, 2024
28bdbc3
Merge pull request #10 from sanger-bentley-group/rename-serotypes
Oliver-Lorenz-dev Mar 5, 2024
2f916a2
Update to reflect current state of the project
HarryHung Apr 3, 2024
b521dd0
Merge pull request #11 from sanger-bentley-group/feature/readme-update
HarryHung Apr 8, 2024
33276fe
add 20B and 24C
Apr 11, 2024
6565c85
add 11F_like to db
Oliver-Lorenz-dev Apr 12, 2024
e5e9178
add 33E
Oliver-Lorenz-dev Apr 14, 2024
42d64f0
add 36A/B
Oliver-Lorenz-dev Apr 15, 2024
9d2b9b1
add 07D
Oliver-Lorenz-dev Apr 15, 2024
914bda3
fix typo in DB
Oliver-Lorenz-dev Apr 18, 2024
a867858
add 15D
Oliver-Lorenz-dev Apr 18, 2024
7281168
add wciZ info
Oliver-Lorenz-dev Apr 18, 2024
6055431
add insertion in whaF
Oliver-Lorenz-dev Apr 19, 2024
5618127
mutations for 24
Oliver-Lorenz-dev Apr 22, 2024
5cece95
add serogroup 19 subtypes
Oliver-Lorenz-dev Apr 29, 2024
34e80d1
remove old files
Oliver-Lorenz-dev Apr 29, 2024
27bae5c
alleles for 19AF
Oliver-Lorenz-dev Apr 30, 2024
0763fa9
subtypes for serogroup 6
Oliver-Lorenz-dev May 9, 2024
ba34205
remove 7D
Oliver-Lorenz-dev May 9, 2024
7449361
tuning serotyping for subgroups
Oliver-Lorenz-dev May 9, 2024
450bb9b
differentiate 6E and 6BIII
Oliver-Lorenz-dev May 20, 2024
cb3f508
remove 6BIII (is 6E oops)
Oliver-Lorenz-dev May 20, 2024
8a7ddb7
improving 6A and 19A subtyping
Oliver-Lorenz-dev May 24, 2024
69593bf
only predict 24A
Oliver-Lorenz-dev May 30, 2024
049de6f
only predict 24A
Oliver-Lorenz-dev May 30, 2024
9dad521
add mutation for 33E
Oliver-Lorenz-dev May 31, 2024
a1da2ae
remove print statement
Oliver-Lorenz-dev May 31, 2024
0e3502b
improve 06 subtyping
Oliver-Lorenz-dev Jun 4, 2024
60318a9
add mutations for 36
Oliver-Lorenz-dev Jun 5, 2024
f5e5da7
improve 19F subtyping
Oliver-Lorenz-dev Jun 5, 2024
3a22ae0
check for wciE truncation in 33E
Oliver-Lorenz-dev Jun 6, 2024
d187cef
add missing mutations for 11E
Oliver-Lorenz-dev Jun 12, 2024
b5a81fa
fix 37 and add dashes to subtypes
Oliver-Lorenz-dev Jun 20, 2024
b9c6cec
remove passes
Oliver-Lorenz-dev Jun 20, 2024
8a21606
custom function for 19F subtypes
Oliver-Lorenz-dev Jul 17, 2024
346051c
Cleaner CSV output files
Oliver-Lorenz-dev Jul 19, 2024
96aa780
add 20A-I
Oliver-Lorenz-dev Jul 22, 2024
6bff43d
add 20C
Oliver-Lorenz-dev Aug 8, 2024
8035a8f
remove passes
Oliver-Lorenz-dev Aug 8, 2024
ca71b03
add disruptive mutation function
Oliver-Lorenz-dev Aug 9, 2024
5d50001
add 33H
Oliver-Lorenz-dev Aug 9, 2024
6216f63
update docs
Oliver-Lorenz-dev Aug 12, 2024
a68dbc7
update docs
Oliver-Lorenz-dev Aug 12, 2024
0e62b9c
update docs
Oliver-Lorenz-dev Aug 12, 2024
b94b2c0
typo
Oliver-Lorenz-dev Aug 13, 2024
4d367d5
Merge pull request #12 from sanger-bentley-group/update-db
Oliver-Lorenz-dev Aug 13, 2024
d484652
2.0.0
Oliver-Lorenz-dev Aug 13, 2024
1ffeae5
Merge pull request #13 from sanger-bentley-group/fix-version
Oliver-Lorenz-dev Aug 13, 2024
3695ab5
add docker instructions
Oliver-Lorenz-dev Sep 5, 2024
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improve 06 subtyping
Oliver-Lorenz-dev committed Jun 4, 2024
commit 0e3502b664ef0f15f3f1defd4ffb99904f390845
2 changes: 2 additions & 0 deletions database/meta.tsv
Original file line number Diff line number Diff line change
@@ -517,6 +517,8 @@ wze 06A 06A 0 allele
wze 06A 06AIV 0 allele
wzg_06AI 06A 06AI 0 allele
wzg_06AI 06A 06AV 0 allele
wzg_06AII 06A 06AII 0 allele
wzg_06AII 06A 06AVI 0 allele
wzg_06B 06A 06B 0 allele
wzg_06BI 06A 06BI 0 allele
wzg_06BII 06A 06BII 0 allele
4 changes: 3 additions & 1 deletion database/streptococcus-pneumoniae-ctvdb/06A.fasta
Original file line number Diff line number Diff line change
@@ -225,4 +225,6 @@ ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCC
>rmlA-5
ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCCGGTTTATGATAAACCCATGATTTACTATCCACTTTCAACATTGATGTTGGCTGGGATTAGGGATATTTTGATAATCTCAACTCCTCAAGATTTGCCTCGTTTTAAAGAGCTTCTTCAAGACGGATCTGAGTTTGGGATTAAACTTTCTTATGCAGAGCAACCAAGTCCAGATGGTTTGGCACAAGCCTTTATCATTGGGGAAGAGTTTATCGGTGACGATAGCGTTGCCTTGATTTTAGGTGACAATATCTACCATGGTCCTGGTCTGAGCACAATGCTTCAAAAAGCAGCCAAGAAAGAGAAAGGTGCGACTGTTTTTGGCTACCATGTCAAGGATCCAGAACGCTTTGGTGTTGTAGAATTTGATGAAAATATGAATGCTATCTCCATCGAAGAAAAGCCAGAATACCCTCGTTCAAACTATGCAGTGACAGGACTCTATTTCTATGATAATGATGTAGTAGAGATTGCCAAAAGTATTAAACCAAGTCCTCGTGGTGAATTGGAAATTACAGATGTCAACAAGGCTTACTTGGATCGTGGTGATTTGTCTGTTGAGCTCATGGGACGTGGTTTTGCTTGGTTGGATACTGGCACTCATGAAAGTTTACTAGAGGCTTCGCAGTACATCGAAACAGTCCAACGGATGCAAAATGTTCAGGTAGCAAACTTAGAAGAAATTGCTTACCGTATGGGCTATATCAGTCGAGAAGATGTATTGGCCTTAGCCCAATCACTTAAGAAAAATGAATACGGACAGTATCTGCTCCGTTTGATTGGAGAAGCATAG
>wzg_06AI
ATGAGTAGACGTTTTAAAAAATCAGGTTCACAGAAAGTGAAGCGAAGTGTTAATATAGTTTTGTTGACTATTTATTTATTGTTAGTTTGTTTTTTATTGTTCTTAATCTTTAAGTACAATATCCTTGCTTTTAGATATCTTAATCTAGTGGTAACTGCGTTAGTCCTACTAGTTGCCTTGGTAGGGCTACTCTTGATTATCTATAAAAAAGCTGAAAAATTTACTATTTTTCTATTGGTGTTTTCTATCCTTGTCAGCTCAGTGTCGCTCTTTGCAGTACAGCAGTTTGTTGGACTGACCAATCGTTTAAATGCGACTTCTAATTACTCAGAATATTCAATCAGTGTCGCTGTTTTAGCAGATAGTGATATCGAAAATGTTACGCAACTGACGAGTGTGACAGCACCGACTGGGACTGATAATGAAAACATTCAAAAACTACTAGCTGATATTAAGTCAAGTCAGAATACCGATTTGACGGTCGACCAGAGTTCGTCTTACTTGGCAGCTTACAAGAGTTTGATTGCAGGGGAGACTAAGGCCATTGTCCTAAATAGTGTCTTTGAAAATATCATCGAGTCAGAGTATCCAGACTACGCATCGAAGATAAAAAAGATTTATACCAAGGGATTCACTAAAAAAGTAGAAGCTCCTAAGACGTCTAAGAATCAGTCTTTCAATATCTATGTTAGTGGAATTGACACCTATGGTCCTATTAGTTCGGTGTCGCGATCAGATGTCAATATCCTGATGACTGTCAATCGAGATACCAAGAAAATCCTCTTGACCACAACGCCACGTGATGCCTATGTACCAATAGCAGATGGTGGAAATAATCAAAAAGATAAATTAACCCATGCGGGTATTTATGGAGTTGATTCGTCCATTCACACCTTAGAAAATCTCTATGGAGTGGATATCAATTACTATGTGCGATTGAACTTCACTTCTTTCTTGAAAATGATTGACTTATTGGGAGGGGTAGATGTTCATAATGATCAAGAGTTTTCAACTCTACATGGGAAGTTCCATTTCCCAGTAGGGAATGTCCATCTAGACTCTGAGCAGGCTCTAGGTTTTGTACGTGAACGCTACTCACTAGCCGATGGAGACCGTGACCGTGGTCGCAACCAACAAAAGGTCATTGTAGCAATTATTAAGAAGTTAACTTCTACAGAGGTTTTGAAAAACTATAGTAGTATTCTTCAAGGATTGCAGGATTCTCTTCAAACAAATATGCCGATTGAGACTATGATAGATTTAGTGAATACTCAGTTGGAAAGTGGAGGGAATTATAAAGTAAATTCGCAAGACTTGAAAGGTACAGGTCGGATGGATCTTCCTTCTTATGCAATGCCAGACAGTAACCTCTATGTGATGGAAGTAGATGATAGTAGTTTAGCTGTAGTTAAAGCAGCTATACAGGATGTGATGGAGGGTAGATGA
ATGAGTAGACGTTTTAAAAAATCAGGTTCACAGAAAGTGAAGCGAAGTGTTAATATAGTTTTGTTGACTATTTATTTATTGTTAGTTTGTTTTTTATTGTTCTTAATCTTTAAGTACAATATCCTTGCTTTTAGATATCTTAATCTAGTGGTAACTGCGTTAGTCCTACTAGTTGCCTTGGTAGGGCTACTCTTGATTATCTATAAAAAAGCTGAAAAATTTACTATTTTTCTATTGGTGTTTTCTATCCTTGTCAGCTCAGTGTCGCTCTTTGCAGTACAGCAGTTTGTTGGACTGACCAATCGTTTAAATGCGACTTCTAATTACTCAGAATATTCAATCAGTGTCGCTGTTTTAGCAGATAGTGATATCGAAAATGTTACGCAACTGACGAGTGTGACAGCACCGACTGGGACTGATAATGAAAACATTCAAAAACTACTAGCTGATATTAAGTCAAGTCAGAATACCGATTTGACGGTCGACCAGAGTTCGTCTTACTTGGCAGCTTACAAGAGTTTGATTGCAGGGGAGACTAAGGCCATTGTCCTAAATAGTGTCTTTGAAAATATCATCGAGTCAGAGTATCCAGACTACGCATCGAAGATAAAAAAGATTTATACCAAGGGATTCACTAAAAAAGTAGAAGCTCCTAAGACGTCTAAGAATCAGTCTTTCAATATCTATGTTAGTGGAATTGACACCTATGGTCCTATTAGTTCGGTGTCGCGATCAGATGTCAATATCCTGATGACTGTCAATCGAGATACCAAGAAAATCCTCTTGACCACAACGCCACGTGATGCCTATGTACCAATAGCAGATGGTGGAAATAATCAAAAAGATAAATTAACCCATGCGGGTATTTATGGAGTTGATTCGTCCATTCACACCTTAGAAAATCTCTATGGAGTGGATATCAATTACTATGTGCGATTGAACTTCACTTCTTTCTTGAAAATGATTGACTTATTGGGAGGGGTAGATGTTCATAATGATCAAGAGTTTTCAACTCTACATGGGAAGTTCCATTTCCCAGTAGGGAATGTCCATCTAGACTCTGAGCAGGCTCTAGGTTTTGTACGTGAACGCTACTCACTAGCCGATGGAGACCGTGACCGTGGTCGCAACCAACAAAAGGTCATTGTAGCAATTATTAAGAAGTTAACTTCTACAGAGGTTTTGAAAAACTATAGTAGTATTCTTCAAGGATTGCAGGATTCTCTTCAAACAAATATGCCGATTGAGACTATGATAGATTTAGTGAATACTCAGTTGGAAAGTGGAGGGAATTATAAAGTAAATTCGCAAGACTTGAAAGGTACAGGTCGGATGGATCTTCCTTCTTATGCAATGCCAGACAGTAACCTCTATGTGATGGAAGTAGATGATAGTAGTTTAGCTGTAGTTAAAGCAGCTATACAGGATGTGATGGAGGGTAGATGA
>wzg_06AII
ATGAGTAGACGTTTTAAAAAATCAGGTTCACAGAAAGTGAAGCGAAGTGTTAATATAGTTTTGTTGACTATTTATTTATTGTTAGTTTGTTTTTTATTGTTCTTAATCTTTAAGTACAATATCCTTGCTTTTAGATATCTTAATCTAGTGGTAACTGCGTTAGTCCTACTAGTTGCCTTGGTAGGGCTACTCCTGATTATCTATAAAAAAGCTGAAAAATTTACTATTTTTCTGTTGGTGTTCTCTATCCTTGTCAGCTCTGTGTCGCTCTTTGCAGTACAGCAGTTTGTTGGACTGACCAATCGTTTAAATGCGACTTCTAATTACTCAGAATATTCAATCAGTGTCGCTGTTTTAGCAGATAGTGAGATCGAAAATGTTACGCAACTGACGAGTGTGACAGCACCGACTGGGACTGATAATGAACATATTCAAAAACTACTAGCTGATATCAAGTCAAGTCAGAATACCGATTTGACGGTCAACCAGAGTTCGTCTTACTTGGCAGCTTACAAGAGTTTGATTGCAGGGGAGACTAAGGCCATTGTCCTAAATAGTGTCTTTGAAAATATCATCGAGTCAGAGTATCCAGACTACGCATCGAAGATAAAAAAGATTTATACCAAGGGATTCACTAAAAAAGTAGAAGCTCCTAAGACGTCTAAGAATCAGTCTTTCAATATCTATGTTAGTGGAATTGACACCTATGGCCCTATTAGTTCGGTGTCGCGATCAGATGTCAATATCCTGATGACTGTCAATCGAGATACCAAGAAAATCCTCTTGACCACAACGCCACGTGATGCCTATGTACCAATCGCAGATGGTGGAAATAATCAAAAAGATAAATTAACCCATGCGGGCATTTATGGAGTTGATTCGTCCATTCACACCTTAGAAAATCTCTATGGAGTGGATATCAATTACTATGTGCGATTGAACTTCACTTCTTTCTTGAAAATGATTGACTTATTGGGAGGAGTAGATGTTCATAATGATCAAGAGTTTTCAACTCTACATGGGAAGTTCCATTTCCCAGTAGGGAATGTCCATCTAGACTCTGAGCAGGCTCTAGGTTTTGTACGTGAACGCTACTCACTAGCCGATGGAGACCGTGACCGTGGTCGCAACCAACAAAAGGTCATTGTAGCAATTATTAAGAAGTTAACTTCTACAGAGGTTTTGAAAAACTATAGTAGTATTCTTCAAGGATTGCAGGATTCTCTTCAAACAAATATGCCGATTGAGACTATGATAGATTTAGTGAATACTCAGTTGGAAAGTGGGGGGAATTATAAAGTAAATTCGCAAGACTTGAAAGGTACAGGTCGGATGGATCTTCCTTCTTATGCAATGCCAGACAGTAACCTCTATGTGATGGAAATAGATGATAGTAGTTTAGCTGTAGTTAAAGCAGCTATACAGGATGTGATGGAGGGTAGATGA
Original file line number Diff line number Diff line change
@@ -223,4 +223,8 @@ ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCC
>rmlA-4
ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCCGGTTTATGATAAACCCATGATTTACTATCCACTTTCAACATTGATGTTGGCTGGGATTAGGGATATTTTGATAATCTCAACTCCTCAAGATTTGCCTCGTTTTAAAGAGCTTCTTCAAGACGGATCTGAGTTTGGGATTAAACTTTCTTATGCAGAGCAACCAAGTCCAGATGGTTTGGCACAAGCCTTTATCATTGGGGAAGAGTTTATTGGTGATGATAGTGTTGCTTTGATCTTGGGGGACAATATCTATCACGGCCCTGGTTTGAGCAAAATGCTTCAAAAAGCAGCCAAGAAAGAGAAAGGTGCGACTGTTTTTGGCTACCATGTCAAGGATCCAGAACGCTTTGGTGTTGTAGAATTTGATGAAAATATGAATGCTATCTCCATCGAAGAAAAGCCAGAATACCCTCGTTCAAACTATGCAGTGACAGGACTCTATTTCTATGATAATGATGTAGTAGAGATTGCCAAAAGTATTAAACCAAGTCCTCGTGGTGAATTGGAAATTACAGATGTCAACAAGGCTTACTTGGATCGTGGTGATTTGTCTGTTGAGCTCATGGGACGTGGTTTTGCTTGGTTGGATACTGGCACTCATGAAAGTTTACTAGAGGCTTCGCAGTACATCGAAACAGTCCAACGGATGCAAAATGTTCAGGTAGCAAACTTAGAAGAAATTGCTTACCGTATGGGCTATATCAGTCGAGAAGATGTATTGGCCTTAGCCCAATCACTTAAGAAAAATGAATACGGACAGTATCTGCTCCGTTTGATTGGAGAAGCATAG
>rmlA-5
ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCCGGTTTATGATAAACCCATGATTTACTATCCACTTTCAACATTGATGTTGGCTGGGATTAGGGATATTTTGATAATCTCAACTCCTCAAGATTTGCCTCGTTTTAAAGAGCTTCTTCAAGACGGATCTGAGTTTGGGATTAAACTTTCTTATGCAGAGCAACCAAGTCCAGATGGTTTGGCACAAGCCTTTATCATTGGGGAAGAGTTTATCGGTGACGATAGCGTTGCCTTGATTTTAGGTGACAATATCTACCATGGTCCTGGTCTGAGCACAATGCTTCAAAAAGCAGCCAAGAAAGAGAAAGGTGCGACTGTTTTTGGCTACCATGTCAAGGATCCAGAACGCTTTGGTGTTGTAGAATTTGATGAAAATATGAATGCTATCTCCATCGAAGAAAAGCCAGAATACCCTCGTTCAAACTATGCAGTGACAGGACTCTATTTCTATGATAATGATGTAGTAGAGATTGCCAAAAGTATTAAACCAAGTCCTCGTGGTGAATTGGAAATTACAGATGTCAACAAGGCTTACTTGGATCGTGGTGATTTGTCTGTTGAGCTCATGGGACGTGGTTTTGCTTGGTTGGATACTGGCACTCATGAAAGTTTACTAGAGGCTTCGCAGTACATCGAAACAGTCCAACGGATGCAAAATGTTCAGGTAGCAAACTTAGAAGAAATTGCTTACCGTATGGGCTATATCAGTCGAGAAGATGTATTGGCCTTAGCCCAATCACTTAAGAAAAATGAATACGGACAGTATCTGCTCCGTTTGATTGGAGAAGCATAG
ATGAAAGGTATTATTCTTGCAGGTGGTTCGGGGACACGATTATATCCTTTGACTCGGGCTGCATCAAAACAACTTATGCCGGTTTATGATAAACCCATGATTTACTATCCACTTTCAACATTGATGTTGGCTGGGATTAGGGATATTTTGATAATCTCAACTCCTCAAGATTTGCCTCGTTTTAAAGAGCTTCTTCAAGACGGATCTGAGTTTGGGATTAAACTTTCTTATGCAGAGCAACCAAGTCCAGATGGTTTGGCACAAGCCTTTATCATTGGGGAAGAGTTTATCGGTGACGATAGCGTTGCCTTGATTTTAGGTGACAATATCTACCATGGTCCTGGTCTGAGCACAATGCTTCAAAAAGCAGCCAAGAAAGAGAAAGGTGCGACTGTTTTTGGCTACCATGTCAAGGATCCAGAACGCTTTGGTGTTGTAGAATTTGATGAAAATATGAATGCTATCTCCATCGAAGAAAAGCCAGAATACCCTCGTTCAAACTATGCAGTGACAGGACTCTATTTCTATGATAATGATGTAGTAGAGATTGCCAAAAGTATTAAACCAAGTCCTCGTGGTGAATTGGAAATTACAGATGTCAACAAGGCTTACTTGGATCGTGGTGATTTGTCTGTTGAGCTCATGGGACGTGGTTTTGCTTGGTTGGATACTGGCACTCATGAAAGTTTACTAGAGGCTTCGCAGTACATCGAAACAGTCCAACGGATGCAAAATGTTCAGGTAGCAAACTTAGAAGAAATTGCTTACCGTATGGGCTATATCAGTCGAGAAGATGTATTGGCCTTAGCCCAATCACTTAAGAAAAATGAATACGGACAGTATCTGCTCCGTTTGATTGGAGAAGCATAG
>wzg_06AI
ATGAGTAGACGTTTTAAAAAATCAGGTTCACAGAAAGTGAAGCGAAGTGTTAATATAGTTTTGTTGACTATTTATTTATTGTTAGTTTGTTTTTTATTGTTCTTAATCTTTAAGTACAATATCCTTGCTTTTAGATATCTTAATCTAGTGGTAACTGCGTTAGTCCTACTAGTTGCCTTGGTAGGGCTACTCTTGATTATCTATAAAAAAGCTGAAAAATTTACTATTTTTCTATTGGTGTTTTCTATCCTTGTCAGCTCAGTGTCGCTCTTTGCAGTACAGCAGTTTGTTGGACTGACCAATCGTTTAAATGCGACTTCTAATTACTCAGAATATTCAATCAGTGTCGCTGTTTTAGCAGATAGTGATATCGAAAATGTTACGCAACTGACGAGTGTGACAGCACCGACTGGGACTGATAATGAAAACATTCAAAAACTACTAGCTGATATTAAGTCAAGTCAGAATACCGATTTGACGGTCGACCAGAGTTCGTCTTACTTGGCAGCTTACAAGAGTTTGATTGCAGGGGAGACTAAGGCCATTGTCCTAAATAGTGTCTTTGAAAATATCATCGAGTCAGAGTATCCAGACTACGCATCGAAGATAAAAAAGATTTATACCAAGGGATTCACTAAAAAAGTAGAAGCTCCTAAGACGTCTAAGAATCAGTCTTTCAATATCTATGTTAGTGGAATTGACACCTATGGTCCTATTAGTTCGGTGTCGCGATCAGATGTCAATATCCTGATGACTGTCAATCGAGATACCAAGAAAATCCTCTTGACCACAACGCCACGTGATGCCTATGTACCAATAGCAGATGGTGGAAATAATCAAAAAGATAAATTAACCCATGCGGGTATTTATGGAGTTGATTCGTCCATTCACACCTTAGAAAATCTCTATGGAGTGGATATCAATTACTATGTGCGATTGAACTTCACTTCTTTCTTGAAAATGATTGACTTATTGGGAGGGGTAGATGTTCATAATGATCAAGAGTTTTCAACTCTACATGGGAAGTTCCATTTCCCAGTAGGGAATGTCCATCTAGACTCTGAGCAGGCTCTAGGTTTTGTACGTGAACGCTACTCACTAGCCGATGGAGACCGTGACCGTGGTCGCAACCAACAAAAGGTCATTGTAGCAATTATTAAGAAGTTAACTTCTACAGAGGTTTTGAAAAACTATAGTAGTATTCTTCAAGGATTGCAGGATTCTCTTCAAACAAATATGCCGATTGAGACTATGATAGATTTAGTGAATACTCAGTTGGAAAGTGGAGGGAATTATAAAGTAAATTCGCAAGACTTGAAAGGTACAGGTCGGATGGATCTTCCTTCTTATGCAATGCCAGACAGTAACCTCTATGTGATGGAAGTAGATGATAGTAGTTTAGCTGTAGTTAAAGCAGCTATACAGGATGTGATGGAGGGTAGATGA
>wzg_06AII
ATGAGTAGACGTTTTAAAAAATCAGGTTCACAGAAAGTGAAGCGAAGTGTTAATATAGTTTTGTTGACTATTTATTTATTGTTAGTTTGTTTTTTATTGTTCTTAATCTTTAAGTACAATATCCTTGCTTTTAGATATCTTAATCTAGTGGTAACTGCGTTAGTCCTACTAGTTGCCTTGGTAGGGCTACTCCTGATTATCTATAAAAAAGCTGAAAAATTTACTATTTTTCTGTTGGTGTTCTCTATCCTTGTCAGCTCTGTGTCGCTCTTTGCAGTACAGCAGTTTGTTGGACTGACCAATCGTTTAAATGCGACTTCTAATTACTCAGAATATTCAATCAGTGTCGCTGTTTTAGCAGATAGTGAGATCGAAAATGTTACGCAACTGACGAGTGTGACAGCACCGACTGGGACTGATAATGAACATATTCAAAAACTACTAGCTGATATCAAGTCAAGTCAGAATACCGATTTGACGGTCAACCAGAGTTCGTCTTACTTGGCAGCTTACAAGAGTTTGATTGCAGGGGAGACTAAGGCCATTGTCCTAAATAGTGTCTTTGAAAATATCATCGAGTCAGAGTATCCAGACTACGCATCGAAGATAAAAAAGATTTATACCAAGGGATTCACTAAAAAAGTAGAAGCTCCTAAGACGTCTAAGAATCAGTCTTTCAATATCTATGTTAGTGGAATTGACACCTATGGCCCTATTAGTTCGGTGTCGCGATCAGATGTCAATATCCTGATGACTGTCAATCGAGATACCAAGAAAATCCTCTTGACCACAACGCCACGTGATGCCTATGTACCAATCGCAGATGGTGGAAATAATCAAAAAGATAAATTAACCCATGCGGGCATTTATGGAGTTGATTCGTCCATTCACACCTTAGAAAATCTCTATGGAGTGGATATCAATTACTATGTGCGATTGAACTTCACTTCTTTCTTGAAAATGATTGACTTATTGGGAGGAGTAGATGTTCATAATGATCAAGAGTTTTCAACTCTACATGGGAAGTTCCATTTCCCAGTAGGGAATGTCCATCTAGACTCTGAGCAGGCTCTAGGTTTTGTACGTGAACGCTACTCACTAGCCGATGGAGACCGTGACCGTGGTCGCAACCAACAAAAGGTCATTGTAGCAATTATTAAGAAGTTAACTTCTACAGAGGTTTTGAAAAACTATAGTAGTATTCTTCAAGGATTGCAGGATTCTCTTCAAACAAATATGCCGATTGAGACTATGATAGATTTAGTGAATACTCAGTTGGAAAGTGGGGGGAATTATAAAGTAAATTCGCAAGACTTGAAAGGTACAGGTCGGATGGATCTTCCTTCTTATGCAATGCCAGACAGTAACCTCTATGTGATGGAAATAGATGATAGTAGTTTAGCTGTAGTTAAAGCAGCTATACAGGATGTGATGGAGGGTAGATGA
12 changes: 6 additions & 6 deletions seroba/serotyping.py
Original file line number Diff line number Diff line change
@@ -166,11 +166,11 @@ def serotype6(assemblie_file,report_file):
# different rml alleles determine the subtypes
elif "rmlB_4" in row_dict and "rmlA_3" in row_dict and "wzg_06AI" in row_dict:
serotype = "06AI"
elif "rmlC_2" in row_dict and "rmlA_2" in row_dict:
elif "rmlC_2" in row_dict and "rmlA_2" in row_dict and "wzy_06AII" in row_dict:
serotype = "06AVI"
elif "rmlA_2" in row_dict and "rmlC_2" not in row_dict and "wzy_06AII" in row_dict:
elif "rmlA_2" in row_dict and "rmlC_2" not in row_dict and "wzy_06AII" in row_dict and "wzg_06AII" in row_dict:
serotype = "06AII"
elif "rmlA_2" in row_dict and "rmlC_2" in row_dict and "wzy_06AII" in row_dict:
elif "rmlA_2" in row_dict and "rmlC_2" in row_dict and "wzy_06AII" in row_dict and "wzg_06AII" in row_dict:
serotype = "06AVI"
elif "rmlA_5" in row_dict and "wzg_06AI" in row_dict:
serotype = "06AV"
@@ -183,11 +183,11 @@ def serotype6(assemblie_file,report_file):
if snp == 'T':
serotype = "06AIV"

# different wzg alleles can determine 6B subgroups
# different wzg and rml alleles can determine 6B subgroups
if serotype == "06B":
if "wzg_06BI" in row_dict:
if "wzg_06BI" in row_dict and "rmlA_4" in row_dict and "rmlB_3" in row_dict:
serotype = "06BI"
elif "wzg_06BII" in row_dict:
elif "wzg_06BII" in row_dict and "rmlA_5" in row_dict and "rmlB_3" in row_dict:
serotype = "06BII"

return serotype