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Merge pull request #217 from ncsa/more-tests
A variety of testing-related changes.
2 parents 5e2e020 + b320b03 commit 56aadef

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‎.github/workflows/python-app.yml‎

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name: NEAT Unit Tests
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name: NEAT Unit and Integration Tests
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on:
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push:
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branches: [develop]
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pull_request:
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branches: [main]
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branches: [main, develop]
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jobs:
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detailed_test_execution:
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tests:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: mamba-org/setup-micromamba@v1
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- name: Checkout
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uses: actions/checkout@v4
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- name: Set up micromamba
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uses: mamba-org/setup-micromamba@v1
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with:
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environment-file: environment.yml
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environment-name: test_neat
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environment-name: neat
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cache-environment: true
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- name: Run unit tests (pytest)
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- name: Install NEAT (with developer dependencies)
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shell: bash -l {0}
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run: |
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micromamba run -n neat poetry install --with dev
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- name: Run unit tests
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shell: bash -l {0}
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run: |
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micromamba run -n neat pytest -q tests
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- name: Run CLI integration test
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shell: bash -l {0}
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run: |
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micromamba run -n test_neat poetry install
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micromamba run -n test_neat pytest -q tests
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micromamba run -n neat pytest -q tests/test_cli

‎CONTRIBUTING.md‎

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Note: Be sure to merge the latest changes before making the pull request. You can increase your chances of a successfull pull request by indicating clearly what branch you are contributing to and making a detailed commit message. It also helps if you open an issue first to let us know you are working on this project.
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Running Tests
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-------
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We use `pytest` for unit and integration tests.
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### Recommended setup
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```bash
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conda env create -f environment.yml
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conda activate neat
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poetry install --with dev
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```
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It will also be necessary to gunzip this file:
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```bash
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gunzip data/H1N1.fa.gz
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```
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To run all tests, use the following command:
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```bash
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pytest -q tests
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```
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It is also possible to run a subset of tests:
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```bash
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pytest -q tests/test_models
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pytest -q tests/test_cli/test_basic_cli.py
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```
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License
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-------
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‎README.md‎

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--incl-fail Include calls that failed filters [False] \
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--fast No equivalent variant detection [False]
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```
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Mappability track examples: https://github.com/zstephens/neat-repeat/tree/master/example_mappabilityTracks
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## Tests
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We provide unit tests (e.g., mutation and sequencing error models) and basic integration tests for the CLI.
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### Run locally
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```bash
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conda env create -f environment.yml
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conda activate neat
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poetry install --with dev
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pytest -q tests
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```
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Please see `CONTRIBUTING.md` for more information and further instructions.
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### Note on Sensitive Patient Data
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ICGC's "Access Controlled Data" documentation can be found at <a href = https://docs.icgc.org/portal/access/ target="_blank">https://docs.icgc.org/portal/access/</a>. To have access to controlled germline data, a DACO must be submitted. Open tier data can be obtained without a DACO, but germline alleles that do not match the reference genome are masked and replaced with the reference allele. Controlled data includes unmasked germline alleles.

‎data/H1N1.fa‎

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>H1N1_HA
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ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTT
3+
ATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGT
4+
TAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGT
5+
AAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGT
6+
CCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGA
7+
GCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGG
8+
CCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAA
9+
ATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGG
10+
GAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAG
11+
AATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAA
12+
GACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAAT
13+
AACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCT
14+
GGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAA
15+
ACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCAC
16+
AAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATT
17+
GCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGC
18+
AGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAA
19+
TTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGA
20+
ATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGG
21+
TTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAG
22+
AAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAAC
23+
ACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACA
24+
GAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGT
25+
CGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTA
26+
CAGTGTAGAATATGTATTTAA
27+
>H1N1_MP
28+
ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGA
29+
TCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAATGGCTAAA
30+
GACAAGACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGT
31+
GAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGG
32+
ATAGAGCAGTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCACT
33+
AAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGAACAGTGACCACA
34+
GAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGATTCACAGCATCGGTCTCACAGAC
35+
AAATGGCTACTACCACCAATCCACTAATCAGGCATGAAAACAGAATGGTGCTGGCTAGCACTACGGCAAA
36+
GGCTATGGAACAGATGGCTGGATCGAGTGAACAGGCAGCAGAGGCCATGGAGGTTGCTAATCAGACTAGG
37+
CAGATGGTACATGCAATGAGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTC
38+
TTGAAAATTTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTCA
39+
TTGCAGCAAATATCATTGGGATCTTGCACCTGATATTGTGGATTACTGATCGTCTTTTTTTCAAATGTAT
40+
TTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCCATGAGGGAA
41+
GAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTAGAGT
42+
AA
43+
>H1N1_NA
44+
ATGAATCCAAACCAAAAGATAATAACCATTGGTTCGGTCTGTATGACAATTGGAATGGCTAACTTAATAT
45+
TACAAATTGGAAACATAATCTCAATATGGATTAGCCACTCAATTCAACTTGGGAATCAAAATCAGATTGA
46+
AACATGCAATCAAAGCGTCATTACTTATGAAAACAACACTTGGGTAAATCAGACATATGTTAACATCAGC
47+
AACACCAACTTTGCTGCTGGACAGTCAGTGGTTTCCGTGAAATTAGCGGGCAATTCCTCTCTCTGCCCTG
48+
TTAGTGGATGGGCTATATACAGTAAAGACAACAGTATAAGAATCGGTTCCAAGGGGGATGTGTTTGTCAT
49+
AAGGGAACCATTCATATCATGCTCCCCCTTGGAATGCAGAACCTTCTTCTTGACTCAAGGGGCCTTGCTA
50+
AATGACAAACATTCCAATGGAACCATTAAAGACAGGAGCCCATATCGAACCCTAATGAGCTGTCCTATTG
51+
GTGAAGTTCCCTCTCCATACAACTCAAGATTTGAGTCAGTCGCTTGGTCAGCAAGTGCTTGTCATGATGG
52+
CATCAATTGGCTAACAATTGGAATTTCTGGCCCAGACAATGGGGCAGTGGCTGTGTTAAAGTACAACGGC
53+
ATAATAACAGACACTATCAAGAGTTGGAGAAACAATATATTGAGAACACAAGAGTCTGAATGTGCATGTG
54+
TAAATGGTTCTTGCTTTACTGTAATGACCGATGGACCAAGTGATGGACAGGCCTCATACAAGATCTTCAG
55+
AATAGAAAAGGGAAAGATAGTCAAATCAGTCGAAATGAATGCCCCTAATTATCACTATGAGGAATGCTCC
56+
TGTTATCCTGATTCTAGTGAAATCACATGTGTGTGCAGGGATAACTGGCATGGCTCGAATCGACCGTGGG
57+
TGTCTTTCAACCAGAATCTGGAATATCAGATAGGATACATATGCAGTGGGATTTTCGGAGACAATCCACG
58+
CCCTAATGATAAGACAGGCAGTTGTGGTCCAGTATCGTCTAATGGAGCAAATGGAGTAAAAGGATTTTCA
59+
TTCAAATACGGCAATGGTGTTTGGATAGGGAGAACTAAAAGCATTAGTTCAAGAAACGGTTTTGAGATGA
60+
TTTGGGATCCGAACGGATGGACTGGGACAGACAATAACTTCTCAATAAAGCAAGATATCGTAGGAATAAA
61+
TGAGTGGTCAGGATATAGCGGGAGTTTTGTTCAGCATCCAGAACTAACAGGGCTGGATTGTATAAGACCT
62+
TGCTTCTGGGTTGAACTAATCAGAGGGCGACCCAAAGAGAACACAATCTGGACTAGCGGGAGCAGCATAT
63+
CCTTTTGTGGTGTAAACAGTGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTTACCAT
64+
TGACAAGTAA
65+
>H1N1_NP
66+
ATGGCGTCTCAAGGCACCAAACGATCATATGAACAAATGGAGACTGGTGGGGAGCGCCAGGATGCCACAG
67+
AAATCAGAGCATCTGTCGGAAGAATGATTGGTGGAATCGGGAGATTCTACATCCAAATGTGCACTGAACT
68+
CAAACTCAGTGATTATGATGGACGACTAATCCAGAATAGCATAACAATAGAGAGGATGGTGCTTTCTGCT
69+
TTTGATGAGAGAAGAAATAAATACCTAGAAGAGCATCCCAGTGCTGGGAAGGACCCTAAGAAAACAGGAG
70+
GACCCATATATAGAAGAATAGACGGAAAGTGGATGAGAGAACTCATCCTTTATGACAAAGAAGAAATAAG
71+
GAGAGTTTGGCGCCAAGCAAACAATGGCGAAGATGCAACAGCAGGTCTTACTCATATCATGATTTGGCAT
72+
TCCAACCTGAATGATGCCACATATCAGAGAACAAGAGCGCTTGTTCGCACCGGAATGGATCCCAGAATGT
73+
GCTCTCTAATGCAAGGTTCAACACTTCCCAGAAGGTCTGGTGCCGCAGGTGCTGCGGTGAAAGGAGTTGG
74+
AACAATAGCAATGGAGTTAATCAGAATGATCAAACGTGGAATCAATGACCGAAATTTCTGGAGGGGTGAA
75+
AATGGACGAAGGACAAGGGTTGCTTATGAAAGAATGTGCAATATCCTCAAAGGAAAATTTCAAACAGCTG
76+
CCCAGAGGGCAATGATGGATCAAGTAAGAGAAAGTCGAAACCCAGGAAACGCTGAGATTGAAGACCTCAT
77+
TTTCCTGGCACGGTCAGCACTCATTCTGAGGGGATCAGTTGCACATAAATCCTGCCTGCCTGCTTGTGTG
78+
TATGGGCTTGCAGTAGCAAGTGGGCATGACTTTGAAAGGGAAGGGTACTCACTGGTCGGGATAGACCCAT
79+
TCAAATTACTCCAAAACAGCCAAGTGGTCAGCCTGATGAGACCAAATGAAAACCCAGCTCACAAGAGTCA
80+
ATTGGTGTGGATGGCATGCCACTCTGCTGCATTTGAAGATTTAAGAGTATCAAGTTTCATAAGAGGAAAG
81+
AAAGTGATTCCAAGAGGAAAGCTTTCCACAAGAGGGGTCCAGATTGCTTCAAATGAGAATGTGGAAACCA
82+
TGGACTCCAATACCCTGGAACTAAGAAGCAGATACTGGGCCATAAGGACCAGGAGTGGAGGAAATACCAA
83+
TCAACAAAAGGCATCCGCAGGCCAGATCAGTGTGCAGCCTACATTCTCAGTGCAGCGAAATCTCCCTTTT
84+
GAAAGAGCAACCGTTATGGCAGCATTCAGCGGGAACAATGAAGGACGGACATCCGACATGCGAACAGAAG
85+
TTATAAGAATGATGGAAAGTGCAAAGCCAGAAGATTTGTCCTTCCAGGGGCGGGGAGTCTTCGAGCTCTC
86+
GGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGGTCTTATTTCTTCGGA
87+
GACAATGCAGAGGAGTATGACAGTTGA
88+
>H1N1_NS
89+
ATGGACTCCAACACCATGTCAAGCTTTCAGGTAGACTGTTTCCTTTGGCATATCCGCAAGCGATTTGCAG
90+
ACAATGGATTGGGTGATGCCCCATTCCTTGATCGGCTCCGCCGAGATCAAAAGTCCTTAAAAGGAAGAGG
91+
CAACACCCTTGGCCTCGATATCGAAACAGCCACTCTTGTTGGGAAACAAATCGTGGAATGGATCTTGAAA
92+
GAGGAATCCAGCGAGACACTTAGAATGACAATTGCATCTGTACCTACTTCGCGCTACCTTTCTGACATGA
93+
CCCTCGAGGAAATGTCACGAGACTGGTTCATGCTCATGCCTAGGCAAAAGATAATAGGCCCTCTTTGCGT
94+
GCGATTGGACCAGGCGGTCATGGAAAAGAACATAGTACTGAAAGCGAACTTCAGTGTAATCTTTAACCGA
95+
TTAGAGACCTTGATACTACTAAGGGCTTTCACTGAGGAGGGAGCAATAGTTGGAGAAATTTCACCATTAC
96+
CTTCTCTTCCAGGACATACTTATGAGGATGTCAAAAATGCAGTTGGGGTCCTCATCGGAGGACTTGAATG
97+
GAATGGTAACACGGTTCGAGTCTCTGAAAATATACAGAGATTCGCTTGGAGAAACTGTGATGAGAATGGG
98+
AGACCTTCACTACCTCCAGAGCAGAAATGAAAAGTGGCGAGAGCAATTGGGACAGAAATTTGAGGAAATA
99+
AGGTGGTTAATTGAAGAAATGCGGCACAGATTGAAAGCGACAGAGAATAGTTTCGAACAAATAACATTTA
100+
TGCAAGCCTTACAACTACTGCTTGAAGTAGAACAAGAGATAAGAGCTTTCTCGTTTCAGCTTATTTAA
101+
>H1N1_PA
102+
ATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAAT
103+
ATGGGGAAGATCCGAAAATCGAAACTAACAAGTTTGCTGCAATATGCACACATTTGGAAGTTTGTTTCAT
104+
GTATTCGGATTTCCATTTCATCGACGAACGGGGTGAATCAATAATTGTAGAATCTGGTGACCCGAATGCA
105+
CTATTGAAGCACCGATTTGAGATAATTGAAGGAAGAGACCGAATCATGGCCTGGACAGTGGTGAACAGTA
106+
TATGTAACACAACAGGGGTAGAGAAGCCTAAATTTCTTCCTGATTTGTATGATTACAAAGAGAACCGGTT
107+
CATTGAAATTGGAGTAACACGGAGGGAAGTCCACATATATTACCTAGAGAAAGCCAACAAAATAAAATCT
108+
GAGAAGACACACATTCACATCTTTTCATTCACTGGAGAGGAGATGGCCACCAAAGCGGACTACACCCTTG
109+
ACGAAGAGAGCAGGGCAAGAATCAAAACTAGGCTTTTCACTATAAGACAAGAAATGGCCAGTAGGAGTCT
110+
ATGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAGACAATTGAAGAAAAATTTGAGATTACAGGAACT
111+
ATGCGCAAGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTAG
112+
ATGGATTCGAGCCGAACGGCTGCATTGAGGGCAAGCTTTCCCAAATGTCAAAAGAAGTGAACGCCAAAAT
113+
TGAACCATTCTTGAGGACGACACCACGCCCCCTCAGATTGCCTGATGGGCCTCTTTGCCATCAGCGGTCA
114+
AAGTTCCTGCTGATGGATGCTCTGAAATTAAGTATTGAAGACCCGAGTCACGAGGGGGAGGGAATACCAC
115+
TATATGATGCAATCAAATGCATGAAGACATTCTTTGGCTGGAAAGAGCCTAACATAGTCAAACCACATGA
116+
GAAAGGCATAAATCCCAATTACCTCATGGCTTGGAAGCAGGTGCTAGCAGAGCTACAGGACATTGAAAAT
117+
GAAGAGAAGATCCCAAGGACAAAGAACATGAAGAGAACAAGCCAATTGAAGTGGGCACTCGGTGAAAATA
118+
TGGCACCAGAAAAAGTAGACTTTGATGACTGCAAAGATGTTGGAGACCTTAAACAGTATGACAGTGATGA
119+
GCCAGAGCCCAGATCTCTAGCAAGCTGGGTCCAAAATGAATTCAATAAGGCATGTGAATTGACTGATTCA
120+
AGCTGGATAGAACTTGATGAAATAGGAGAAGATGTTGCCCCGATTGAACATATCGCAAGCATGAGGAGGA
121+
ACTATTTTACAGCAGAAGTGTCCCACTGCAGGGCTACTGAATACATAATGAAGGGAGTGTACATAAATAC
122+
GGCCTTGCTCAATGCATCCTGTGCAGCCATGGATGACTTTCAGCTGATCCCAATGATAAGCAAATGTAGG
123+
ACCAAAGAAGGAAGACGGAAAACAAACCTGTATGGGTTCATTATAAAAGGAAGGTCTCATTTGAGAAATG
124+
ATACTGATGTGGTGAACTTTGTAAGTATGGAGTTCTCACTCACTGACCCGAGACTGGAGCCACACAAATG
125+
GGAAAAATACTGTGTTCTTGAAATAGGAGACATGCTCTTGAGGACTGCGATAGGCCAAGTGTCGAGGCCC
126+
ATGTTCCTATATGTGAGAACCAATGGAACCTCCAAGATCAAGATGAAATGGGGCATGGAAATGAGGCGCT
127+
GCCTTCTTCAGTCTCTTCAGCAGATTGAGAGCATGATTGAGGCCGAGTCTTCTGTCAAAGAGAAAGACAT
128+
GACCAAGGAATTCTTTGAAAACAAATCGGAAACATGGCCAATCGGAGAGTCACCCAGGGGAGTGGAGGAA
129+
GGCTCTATTGGGAAAGTGTGCAGGACCTTACTGGCAAAATCTGTATTCAACAGTCTATATGCGTCTCCAC
130+
AACTTGAGGGGTTTTCGGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGA
131+
ACCTGGAACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTGGGTT
132+
TTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAGTAG
133+
>H1N1_PB1
134+
ATGGATGTCAATCCGACTCTACTTTTCCTAAAAATTCCAGCGCAAAATGCCATAAGCACCACATTCCCTT
135+
ATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTAAACAGAACACA
136+
CCAATACTCAGAAAAGGGAAAGTGGACGACAAACACAGAGACTGGTGCACCCCAGCTCAACCCGATTGAT
137+
GGACCACTACCTGAGGATAATGAACCAAGTGGGTATGCACAAACAGACTGTGTTCTAGAGGCTATGGCTT
138+
TCCTTGAAGAATCCCACCCAGGAATATTTGAGAATTCATGCCTTGAAACAATGGAAGTTGTTCAACAAAC
139+
AAGGGTAGATAAACTAACTCAAGGTCGCCAGACTTATGATTGGACATTAAACAGAAATCAACCGGCAGCA
140+
ACTGCATTGGCCAACACCATAGAAGTCTTTAGATCGAATGGCCTAACAGCTAATGAGTCAGGAAGGCTAA
141+
TAGATTTCTTAAAGGATGTAATGGAATCAATGAACAAAGAGGAAATAGAGATAACAACCCACTTTCAAAG
142+
AAAAAGGAGAGTAAGAGACAACATGACCAAGAAGATGGTCACGCAAAGAACAATAGGGAAGAAAAAACAA
143+
AGACTGAATAAGAGAGGCTATCTAATAAGAGCACTGACATTAAATACGATGACCAAAGATGCAGAGAGAG
144+
GCAAGTTAAAAAGAAGGGCTATCGCAACACCTGGGATGCAGATTAGAGGTTTCGTATACTTTGTTGAAAC
145+
TTTAGCTAGGAGCATTTGCGAAAAGCTTGAACAGTCTGGGCTCCCAGTAGGGGGCAATGAAAAGAAGGCC
146+
AAACTGGCAAATGTTGTGAGAAAGATGATGACTAATTCACAAGACACAGAGATTTCTTTCACAATCACTG
147+
GGGACAACACTAAGTGGAATGAAAATCAAAATCCTCGAATGTTCCTGGCGATGATTACATATATCACCAG
148+
AAATCAACCCGAGTGGTTCAGAAACATCCTGAGCATGGCACCCATAATGTTCTCAAACAAAATGGCAAGA
149+
CTAGGGAAAGGGTACATGTTCGAGAGTAAAAGAATGAAGATTCGAACACAAATACCAGCAGAAATGCTAG
150+
CAAGCATTGACCTGAAGTACTTCAATGAATCAACAAAGAAGAAAATTGAGAAAATAAGGCCTCTTCTAAT
151+
AGATGGCACAGCATCACTGAGTCCTGGGATGATGATGGGCATGTTCAACATGCTAAGTACGGTCTTGGGA
152+
GTCTCGATACTGAATCTTGGACAAAAGAAATACACCAAGACAATATACTGGTGGGATGGGCTCCAATCAT
153+
CCGACGATTTTGCTCTCATAGTGAATGCACCAAACCATGAGGGAATACAAGCAGGAGTGGACAGATTCTA
154+
CAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAGACAGGGACATTT
155+
GAATTCACAAGCTTTTTTTATCGCTATGGATTTGTGGCTAATTTTAGCATGGAGCTACCCAGCTTTGGAG
156+
TGTCTGGAGTAAATGAATCAGCTGACATGAGTATTGGAGTAACAGTGATAAAGAACAACATGATAAACAA
157+
TGACCTTGGACCTGCAACGGCCCAGATGGCTCTTCAATTGTTCATCAAAGACTACAGATACACATATAGG
158+
TGCCATAGGGGAGACACACAAATTCAGACGAGAAGATCATTTGAGTTAAAGAAGCTGTGGGATCAAACCC
159+
AATCAAAGGTAGGGCTATTAGTATCAGATGGAGGACCAAACTTATACAATATACGGAATCTTCACATTCC
160+
TGAAGTCTGCTTAAAATGGGAGCTAATGGATGATGATTATCGGGGAAGACTTTGTAATCCCCTGAATCCC
161+
TTTGTCAGTCATAAAGAGATTGATTCTGTAAACAATGCTGTGGTAATGCCAGCCCATGGTCCAGCCAAAA
162+
GCATGGAATATGATGCCGTTGCAACTACACATTCCTGGATTCCCAAGAGGAATCGTTCTATTCTCAACAC
163+
AAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAATCTATTCGAGAAATTTTTC
164+
CCTAGCAGTTCATATAGGAGACCGGTTGGAATTTCTAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGA
165+
TTGATGCCAGGGTCGACTTCGAGTCTGGACGGATCAAGAAAGAAGAGTTCTCTGAGATCATGAAGATCTG
166+
TTCCACCATTGAAGAACTCAGACGGCAAAAATAA
167+
>H1N1_PB2
168+
ATGGAGAGAATAAAAGAACTGAGAGATCTAATGTCGCAGTCCCGCACTCGCGAGATACTCACTAAGACCA
169+
CTGTGGACCATATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCCCGCACTCAGAAT
170+
GAAGTGGATGATGGCAATGAGATACCCAATTACAGCAGACAAGAGAATAATGGACATGATTCCAGAGAGG
171+
AATGAACAAGGACAAACCCTCTGGAGCAAAACAAACGATGCTGGATCAGACCGAGTGATGGTATCACCTC
172+
TGGCCGTAACATGGTGGAATAGGAATGGCCCAACAACAAGTACAGTTCATTACCCTAAGGTATATAAAAC
173+
TTATTTCGAAAAGGTCGAAAGGTTGAAACATGGTACCTTCGGCCCTGTCCACTTCAGAAATCAAGTTAAA
174+
ATAAGGAGGAGAGTTGATACAAACCCTGGCCATGCAGATCTCAGTGCCAAGGAGGCACAGGATGTGATTA
175+
TGGAAGTTGTTTTCCCAAATGAAGTGGGGGCAAGAATACTGACATCAGAGTCACAGCTGGCAATAACAAA
176+
AGAGAAGAAAGAAGAGCTCCAGGATTGTAAAATTGCTCCCTTGATGGTGGCGTACATGCTAGAAAGAGAA
177+
TTGGTCCGTAAAACAAGGTTTCTCCCAGTAGCCGGCGGAACAGGCAGTGTTTATATTGAAGTGTTGCACT
178+
TAACCCAAGGGACGTGCTGGGAGCAGATGTACACTCCAGGAGGAGAAGTGAGAAATGATGATGTTGACCA
179+
AAGTTTGATTATCGCTGCTAGAAACATAGTAAGAAGAGCAGCAGTGTCAGCAGACCCATTAGCATCTCTC
180+
TTGGAAATGTGCCACAGCACACAGATTGGAGGAGTAAGGATGGTGGACATCCTTAGACAGAATCCAACTG
181+
AGGAACAAGCCGTAGACATATGCAAGGCAGCAATAGGGTTGAGGATTAGCTCATCTTTCAGTTTTGGTGG
182+
GTTCACTTTCAAAAGGACAAGCGGATCATCAGTCAAGAAAGAAGAAGAAGTGCTAACGGGCAACCTCCAA
183+
ACACTGAAAATAAGAGTACATGAAGGGTATGAAGAATTCACAATGGTTGGGAGAAGAGCAACAGCTATTC
184+
TCAGAAAGGCAACCAGGAGATTGATCCAGTTGATAGTAAGCGGGAGAGACGAGCAGTCAATTGCTGAGGC
185+
AATAATTGTGGCCATGGTATTCTCACAAGAGGATTGCATGATCAAGGCAGTTAGGGGCGATCTGAACTTT
186+
GTCAATAGGGCAAACCAGCGACTGAACCCCATGCACCAACTCTTGAGGCATTTCCAAAAAGATGCAAAAG
187+
TGCTTTTCCAGAACTGGGGAATTGAATCCATCGACAATGTGATGGGAATGATCGGAATACTGCCCGACAT
188+
GACCCCAAGCACGGAGATGTCGCTGAGAGGGATAAGAGTCAGCAAAATGGGAGTAGATGAATACTCCAGC
189+
ACGGAGAGAGTGGTAGTGAGTATTGACCGATTTTTAAGGGTTAGAGATCAAAGAGGGAACGTACTATTGT
190+
CTCCCGAAGAAGTCAGTGAAACGCAAGGAACTGAGAAGTTGACAATAACTTATTCGTCATCAATGATGTG
191+
GGAGATCAATGGCCCTGAGTCAGTGCTAGTCAACACTTATCAATGGATAATCAGGAACTGGGAAATTGTG
192+
AAAATTCAATGGTCACAAGATCCCACAATGTTATACAACAAAATGGAATTTGAACCATTTCAGTCTCTTG
193+
TCCCTAAGGCAACCAGAAGCCGGTACAGTGGATTCGTAAGGACACTGTTCCAGCAAATGCGGGATGTGCT
194+
TGGGACATTTGACACTGTCCAAATAATAAAACTTCTCCCCTTTGCTGCTGCTCCACCAGAACAGAGTAGG
195+
ATGCAATTTTCCTCATTGACTGTGAATGTGAGAGGATCAGGGTTGAGGATACTGGTAAGAGGCAATTCTC
196+
CAGTATTCAATTACAACAAGGCAACCAAACGACTTACAGTTCTTGGAAAGGATGCAGGTGCATTGACTGA
197+
AGATCCAGATGAAGGCACATCTGGGGTGGAGTCTGCTGTCCTGAGAGGATTTCTCATTTTGGGCAAAGAA
198+
GACAAGAGATATGGCCCAGCATTAAGCATCAATGAACTGAGCAATCTTGCAAAAGGAGAGAAGGCTAATG
199+
TGCTAATTGGGCAAGGGGACGTAGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACTGACAG
200+
CCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAG

‎data/H1N1.fa.gz‎

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‎environment.yml‎

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name: neat
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3+
channels:
4+
- bioconda
5+
- conda-forge
6+
37
dependencies:
48
- python==3.11.*
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- pip

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