A variety of testing-related changes.

.github/workflows/python-app.yml

@@ -1,21 +1,36 @@
-name: NEAT Unit Tests
+name: NEAT Unit and Integration Tests
 
 on:
+  push:
+    branches: [develop]
   pull_request:
-    branches: [main]
+    branches: [main, develop]
 
 jobs:
-  detailed_test_execution:
+  tests:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: mamba-org/setup-micromamba@v1
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up micromamba
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: environment.yml
-          environment-name: test_neat
+          environment-name: neat
           cache-environment: true
 
-      - name: Run unit tests (pytest)
+      - name: Install NEAT (with developer dependencies)
+        shell: bash -l {0}
+        run: |
+          micromamba run -n neat poetry install --with dev
+
+      - name: Run unit tests
+        shell: bash -l {0}
+        run: |
+          micromamba run -n neat pytest -q tests
+
+      - name: Run CLI integration test
+        shell: bash -l {0}
         run: |
-          micromamba run -n test_neat poetry install
-          micromamba run -n test_neat pytest -q tests
+          micromamba run -n neat pytest -q tests/test_cli

CONTRIBUTING.md

@@ -23,6 +23,37 @@ In general, we follow the "fork-and-pull" Git workflow.
 
 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.
 
+Running Tests
+-------
+
+We use `pytest` for unit and integration tests.
+
+### Recommended setup
+```bash
+conda env create -f environment.yml
+conda activate neat
+poetry install --with dev
+```
+
+It will also be necessary to gunzip this file:
+
+```bash
+gunzip data/H1N1.fa.gz
+```
+
+To run all tests, use the following command:
+
+```bash
+pytest -q tests
+```
+
+It is also possible to run a subset of tests:
+
+```bash
+pytest -q tests/test_models
+pytest -q tests/test_cli/test_basic_cli.py
+```
+
 License
 -------
 

README.md

@@ -432,7 +432,20 @@ neat vcf_compare
         --incl-fail        Include calls that failed filters [False]   \
         --fast             No equivalent variant detection [False]
 ```
-Mappability track examples: https://github.com/zstephens/neat-repeat/tree/master/example_mappabilityTracks
+
+## Tests
+
+We provide unit tests (e.g., mutation and sequencing error models) and basic integration tests for the CLI.
+
+### Run locally
+```bash
+conda env create -f environment.yml
+conda activate neat
+poetry install --with dev
+pytest -q tests
+```
+
+Please see `CONTRIBUTING.md` for more information and further instructions.
 
 ### Note on Sensitive Patient Data
 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

@@ -0,0 +1,200 @@
+>H1N1_HA
+ATGAAGGCAATACTAGTAGTTCTGCTATATACATTTGCAACCGCAAATGCAGACACATTATGTATAGGTT
+ATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGT
+TAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGT
+AAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGT
+CCTACATTGTGGAAACATCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGA
+GCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGG
+CCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAA
+ATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGG
+GAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTCTCTATCAG
+AATGCAGATGCATATGTTTTTGTGGGGACATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAA
+GACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAAT
+AACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCT
+GGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAGACACCCAAGGGTGCTATAA
+ACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTAAAAAGCAC
+AAAATTGAGACTGGCCACAGGATTGAGGAATGTCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATT
+GCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGC
+AGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAA
+TTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGA
+ATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGG
+TTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAG
+AAGCCAGTTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAAC
+ACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACA
+GAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGT
+CGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTA
+CAGTGTAGAATATGTATTTAA
+>H1N1_MP
+ATGAGTCTTCTAACCGAGGTCGAAACGTACGTTCTTTCTATCATCCCGTCAGGCCCCCTCAAAGCCGAGA
+TCGCGCAGAGACTGGAAAGTGTCTTTGCAGGAAAGAACACAGATCTTGAGGCTCTCATGGAATGGCTAAA
+GACAAGACCAATCTTGTCACCTCTGACTAAGGGAATTTTAGGATTTGTGTTCACGCTCACCGTGCCCAGT
+GAGCGAGGACTGCAGCGTAGACGCTTTGTCCAAAATGCCCTAAATGGGAATGGGGACCCGAACAACATGG
+ATAGAGCAGTTAAACTATACAAGAAGCTCAAAAGAGAAATAACGTTCCATGGGGCCAAGGAGGTGTCACT
+AAGCTATTCAACTGGTGCACTTGCCAGTTGCATGGGCCTCATATACAACAGGATGGGAACAGTGACCACA
+GAAGCTGCTTTTGGTCTAGTGTGTGCCACTTGTGAACAGATTGCTGATTCACAGCATCGGTCTCACAGAC
+AAATGGCTACTACCACCAATCCACTAATCAGGCATGAAAACAGAATGGTGCTGGCTAGCACTACGGCAAA
+GGCTATGGAACAGATGGCTGGATCGAGTGAACAGGCAGCAGAGGCCATGGAGGTTGCTAATCAGACTAGG
+CAGATGGTACATGCAATGAGAACTATTGGGACTCATCCTAGCTCCAGTGCTGGTCTGAAAGATGACCTTC
+TTGAAAATTTGCAGGCCTACCAGAAGCGAATGGGAGTGCAGATGCAGCGATTCAAGTGATCCTCTCGTCA
+TTGCAGCAAATATCATTGGGATCTTGCACCTGATATTGTGGATTACTGATCGTCTTTTTTTCAAATGTAT
+TTATCGTCGCTTTAAATACGGTTTGAAAAGAGGGCCTTCTACGGAAGGAGTGCCTGAGTCCATGAGGGAA
+GAATATCAACAGGAACAGCAGAGTGCTGTGGATGTTGACGATGGTCATTTTGTCAACATAGAGCTAGAGT
+AA
+>H1N1_NA
+ATGAATCCAAACCAAAAGATAATAACCATTGGTTCGGTCTGTATGACAATTGGAATGGCTAACTTAATAT
+TACAAATTGGAAACATAATCTCAATATGGATTAGCCACTCAATTCAACTTGGGAATCAAAATCAGATTGA
+AACATGCAATCAAAGCGTCATTACTTATGAAAACAACACTTGGGTAAATCAGACATATGTTAACATCAGC
+AACACCAACTTTGCTGCTGGACAGTCAGTGGTTTCCGTGAAATTAGCGGGCAATTCCTCTCTCTGCCCTG
+TTAGTGGATGGGCTATATACAGTAAAGACAACAGTATAAGAATCGGTTCCAAGGGGGATGTGTTTGTCAT
+AAGGGAACCATTCATATCATGCTCCCCCTTGGAATGCAGAACCTTCTTCTTGACTCAAGGGGCCTTGCTA
+AATGACAAACATTCCAATGGAACCATTAAAGACAGGAGCCCATATCGAACCCTAATGAGCTGTCCTATTG
+GTGAAGTTCCCTCTCCATACAACTCAAGATTTGAGTCAGTCGCTTGGTCAGCAAGTGCTTGTCATGATGG
+CATCAATTGGCTAACAATTGGAATTTCTGGCCCAGACAATGGGGCAGTGGCTGTGTTAAAGTACAACGGC
+ATAATAACAGACACTATCAAGAGTTGGAGAAACAATATATTGAGAACACAAGAGTCTGAATGTGCATGTG
+TAAATGGTTCTTGCTTTACTGTAATGACCGATGGACCAAGTGATGGACAGGCCTCATACAAGATCTTCAG
+AATAGAAAAGGGAAAGATAGTCAAATCAGTCGAAATGAATGCCCCTAATTATCACTATGAGGAATGCTCC
+TGTTATCCTGATTCTAGTGAAATCACATGTGTGTGCAGGGATAACTGGCATGGCTCGAATCGACCGTGGG
+TGTCTTTCAACCAGAATCTGGAATATCAGATAGGATACATATGCAGTGGGATTTTCGGAGACAATCCACG
+CCCTAATGATAAGACAGGCAGTTGTGGTCCAGTATCGTCTAATGGAGCAAATGGAGTAAAAGGATTTTCA
+TTCAAATACGGCAATGGTGTTTGGATAGGGAGAACTAAAAGCATTAGTTCAAGAAACGGTTTTGAGATGA
+TTTGGGATCCGAACGGATGGACTGGGACAGACAATAACTTCTCAATAAAGCAAGATATCGTAGGAATAAA
+TGAGTGGTCAGGATATAGCGGGAGTTTTGTTCAGCATCCAGAACTAACAGGGCTGGATTGTATAAGACCT
+TGCTTCTGGGTTGAACTAATCAGAGGGCGACCCAAAGAGAACACAATCTGGACTAGCGGGAGCAGCATAT
+CCTTTTGTGGTGTAAACAGTGACACTGTGGGTTGGTCTTGGCCAGACGGTGCTGAGTTGCCATTTACCAT
+TGACAAGTAA
+>H1N1_NP
+ATGGCGTCTCAAGGCACCAAACGATCATATGAACAAATGGAGACTGGTGGGGAGCGCCAGGATGCCACAG
+AAATCAGAGCATCTGTCGGAAGAATGATTGGTGGAATCGGGAGATTCTACATCCAAATGTGCACTGAACT
+CAAACTCAGTGATTATGATGGACGACTAATCCAGAATAGCATAACAATAGAGAGGATGGTGCTTTCTGCT
+TTTGATGAGAGAAGAAATAAATACCTAGAAGAGCATCCCAGTGCTGGGAAGGACCCTAAGAAAACAGGAG
+GACCCATATATAGAAGAATAGACGGAAAGTGGATGAGAGAACTCATCCTTTATGACAAAGAAGAAATAAG
+GAGAGTTTGGCGCCAAGCAAACAATGGCGAAGATGCAACAGCAGGTCTTACTCATATCATGATTTGGCAT
+TCCAACCTGAATGATGCCACATATCAGAGAACAAGAGCGCTTGTTCGCACCGGAATGGATCCCAGAATGT
+GCTCTCTAATGCAAGGTTCAACACTTCCCAGAAGGTCTGGTGCCGCAGGTGCTGCGGTGAAAGGAGTTGG
+AACAATAGCAATGGAGTTAATCAGAATGATCAAACGTGGAATCAATGACCGAAATTTCTGGAGGGGTGAA
+AATGGACGAAGGACAAGGGTTGCTTATGAAAGAATGTGCAATATCCTCAAAGGAAAATTTCAAACAGCTG
+CCCAGAGGGCAATGATGGATCAAGTAAGAGAAAGTCGAAACCCAGGAAACGCTGAGATTGAAGACCTCAT
+TTTCCTGGCACGGTCAGCACTCATTCTGAGGGGATCAGTTGCACATAAATCCTGCCTGCCTGCTTGTGTG
+TATGGGCTTGCAGTAGCAAGTGGGCATGACTTTGAAAGGGAAGGGTACTCACTGGTCGGGATAGACCCAT
+TCAAATTACTCCAAAACAGCCAAGTGGTCAGCCTGATGAGACCAAATGAAAACCCAGCTCACAAGAGTCA
+ATTGGTGTGGATGGCATGCCACTCTGCTGCATTTGAAGATTTAAGAGTATCAAGTTTCATAAGAGGAAAG
+AAAGTGATTCCAAGAGGAAAGCTTTCCACAAGAGGGGTCCAGATTGCTTCAAATGAGAATGTGGAAACCA
+TGGACTCCAATACCCTGGAACTAAGAAGCAGATACTGGGCCATAAGGACCAGGAGTGGAGGAAATACCAA
+TCAACAAAAGGCATCCGCAGGCCAGATCAGTGTGCAGCCTACATTCTCAGTGCAGCGAAATCTCCCTTTT
+GAAAGAGCAACCGTTATGGCAGCATTCAGCGGGAACAATGAAGGACGGACATCCGACATGCGAACAGAAG
+TTATAAGAATGATGGAAAGTGCAAAGCCAGAAGATTTGTCCTTCCAGGGGCGGGGAGTCTTCGAGCTCTC
+GGACGAAAAGGCAACGAACCCGATCGTGCCTTCCTTTGACATGAGTAATGAAGGGTCTTATTTCTTCGGA
+GACAATGCAGAGGAGTATGACAGTTGA
+>H1N1_NS
+ATGGACTCCAACACCATGTCAAGCTTTCAGGTAGACTGTTTCCTTTGGCATATCCGCAAGCGATTTGCAG
+ACAATGGATTGGGTGATGCCCCATTCCTTGATCGGCTCCGCCGAGATCAAAAGTCCTTAAAAGGAAGAGG
+CAACACCCTTGGCCTCGATATCGAAACAGCCACTCTTGTTGGGAAACAAATCGTGGAATGGATCTTGAAA
+GAGGAATCCAGCGAGACACTTAGAATGACAATTGCATCTGTACCTACTTCGCGCTACCTTTCTGACATGA
+CCCTCGAGGAAATGTCACGAGACTGGTTCATGCTCATGCCTAGGCAAAAGATAATAGGCCCTCTTTGCGT
+GCGATTGGACCAGGCGGTCATGGAAAAGAACATAGTACTGAAAGCGAACTTCAGTGTAATCTTTAACCGA
+TTAGAGACCTTGATACTACTAAGGGCTTTCACTGAGGAGGGAGCAATAGTTGGAGAAATTTCACCATTAC
+CTTCTCTTCCAGGACATACTTATGAGGATGTCAAAAATGCAGTTGGGGTCCTCATCGGAGGACTTGAATG
+GAATGGTAACACGGTTCGAGTCTCTGAAAATATACAGAGATTCGCTTGGAGAAACTGTGATGAGAATGGG
+AGACCTTCACTACCTCCAGAGCAGAAATGAAAAGTGGCGAGAGCAATTGGGACAGAAATTTGAGGAAATA
+AGGTGGTTAATTGAAGAAATGCGGCACAGATTGAAAGCGACAGAGAATAGTTTCGAACAAATAACATTTA
+TGCAAGCCTTACAACTACTGCTTGAAGTAGAACAAGAGATAAGAGCTTTCTCGTTTCAGCTTATTTAA
+>H1N1_PA
+ATGGAAGACTTTGTGCGACAATGCTTCAATCCAATGATCGTCGAGCTTGCGGAAAAGGCAATGAAAGAAT
+ATGGGGAAGATCCGAAAATCGAAACTAACAAGTTTGCTGCAATATGCACACATTTGGAAGTTTGTTTCAT
+GTATTCGGATTTCCATTTCATCGACGAACGGGGTGAATCAATAATTGTAGAATCTGGTGACCCGAATGCA
+CTATTGAAGCACCGATTTGAGATAATTGAAGGAAGAGACCGAATCATGGCCTGGACAGTGGTGAACAGTA
+TATGTAACACAACAGGGGTAGAGAAGCCTAAATTTCTTCCTGATTTGTATGATTACAAAGAGAACCGGTT
+CATTGAAATTGGAGTAACACGGAGGGAAGTCCACATATATTACCTAGAGAAAGCCAACAAAATAAAATCT
+GAGAAGACACACATTCACATCTTTTCATTCACTGGAGAGGAGATGGCCACCAAAGCGGACTACACCCTTG
+ACGAAGAGAGCAGGGCAAGAATCAAAACTAGGCTTTTCACTATAAGACAAGAAATGGCCAGTAGGAGTCT
+ATGGGATTCCTTTCGTCAGTCCGAAAGAGGCGAAGAGACAATTGAAGAAAAATTTGAGATTACAGGAACT
+ATGCGCAAGCTTGCCGACCAAAGTCTCCCACCGAACTTCTCCAGCCTTGAAAACTTTAGAGCCTATGTAG
+ATGGATTCGAGCCGAACGGCTGCATTGAGGGCAAGCTTTCCCAAATGTCAAAAGAAGTGAACGCCAAAAT
+TGAACCATTCTTGAGGACGACACCACGCCCCCTCAGATTGCCTGATGGGCCTCTTTGCCATCAGCGGTCA
+AAGTTCCTGCTGATGGATGCTCTGAAATTAAGTATTGAAGACCCGAGTCACGAGGGGGAGGGAATACCAC
+TATATGATGCAATCAAATGCATGAAGACATTCTTTGGCTGGAAAGAGCCTAACATAGTCAAACCACATGA
+GAAAGGCATAAATCCCAATTACCTCATGGCTTGGAAGCAGGTGCTAGCAGAGCTACAGGACATTGAAAAT
+GAAGAGAAGATCCCAAGGACAAAGAACATGAAGAGAACAAGCCAATTGAAGTGGGCACTCGGTGAAAATA
+TGGCACCAGAAAAAGTAGACTTTGATGACTGCAAAGATGTTGGAGACCTTAAACAGTATGACAGTGATGA
+GCCAGAGCCCAGATCTCTAGCAAGCTGGGTCCAAAATGAATTCAATAAGGCATGTGAATTGACTGATTCA
+AGCTGGATAGAACTTGATGAAATAGGAGAAGATGTTGCCCCGATTGAACATATCGCAAGCATGAGGAGGA
+ACTATTTTACAGCAGAAGTGTCCCACTGCAGGGCTACTGAATACATAATGAAGGGAGTGTACATAAATAC
+GGCCTTGCTCAATGCATCCTGTGCAGCCATGGATGACTTTCAGCTGATCCCAATGATAAGCAAATGTAGG
+ACCAAAGAAGGAAGACGGAAAACAAACCTGTATGGGTTCATTATAAAAGGAAGGTCTCATTTGAGAAATG
+ATACTGATGTGGTGAACTTTGTAAGTATGGAGTTCTCACTCACTGACCCGAGACTGGAGCCACACAAATG
+GGAAAAATACTGTGTTCTTGAAATAGGAGACATGCTCTTGAGGACTGCGATAGGCCAAGTGTCGAGGCCC
+ATGTTCCTATATGTGAGAACCAATGGAACCTCCAAGATCAAGATGAAATGGGGCATGGAAATGAGGCGCT
+GCCTTCTTCAGTCTCTTCAGCAGATTGAGAGCATGATTGAGGCCGAGTCTTCTGTCAAAGAGAAAGACAT
+GACCAAGGAATTCTTTGAAAACAAATCGGAAACATGGCCAATCGGAGAGTCACCCAGGGGAGTGGAGGAA
+GGCTCTATTGGGAAAGTGTGCAGGACCTTACTGGCAAAATCTGTATTCAACAGTCTATATGCGTCTCCAC
+AACTTGAGGGGTTTTCGGCTGAATCGAGAAAATTGCTTCTCATTGTTCAGGCACTTAGGGACAACCTGGA
+ACCTGGAACCTTCGATCTTGGGGGGCTATATGAAGCAATCGAGGAGTGCCTGATTAATGATCCCTGGGTT
+TTGCTTAATGCATCTTGGTTCAACTCCTTCCTCACACATGCACTGAAGTAG
+>H1N1_PB1
+ATGGATGTCAATCCGACTCTACTTTTCCTAAAAATTCCAGCGCAAAATGCCATAAGCACCACATTCCCTT
+ATACTGGAGATCCTCCATACAGCCATGGAACAGGAACAGGATACACCATGGACACAGTAAACAGAACACA
+CCAATACTCAGAAAAGGGAAAGTGGACGACAAACACAGAGACTGGTGCACCCCAGCTCAACCCGATTGAT
+GGACCACTACCTGAGGATAATGAACCAAGTGGGTATGCACAAACAGACTGTGTTCTAGAGGCTATGGCTT
+TCCTTGAAGAATCCCACCCAGGAATATTTGAGAATTCATGCCTTGAAACAATGGAAGTTGTTCAACAAAC
+AAGGGTAGATAAACTAACTCAAGGTCGCCAGACTTATGATTGGACATTAAACAGAAATCAACCGGCAGCA
+ACTGCATTGGCCAACACCATAGAAGTCTTTAGATCGAATGGCCTAACAGCTAATGAGTCAGGAAGGCTAA
+TAGATTTCTTAAAGGATGTAATGGAATCAATGAACAAAGAGGAAATAGAGATAACAACCCACTTTCAAAG
+AAAAAGGAGAGTAAGAGACAACATGACCAAGAAGATGGTCACGCAAAGAACAATAGGGAAGAAAAAACAA
+AGACTGAATAAGAGAGGCTATCTAATAAGAGCACTGACATTAAATACGATGACCAAAGATGCAGAGAGAG
+GCAAGTTAAAAAGAAGGGCTATCGCAACACCTGGGATGCAGATTAGAGGTTTCGTATACTTTGTTGAAAC
+TTTAGCTAGGAGCATTTGCGAAAAGCTTGAACAGTCTGGGCTCCCAGTAGGGGGCAATGAAAAGAAGGCC
+AAACTGGCAAATGTTGTGAGAAAGATGATGACTAATTCACAAGACACAGAGATTTCTTTCACAATCACTG
+GGGACAACACTAAGTGGAATGAAAATCAAAATCCTCGAATGTTCCTGGCGATGATTACATATATCACCAG
+AAATCAACCCGAGTGGTTCAGAAACATCCTGAGCATGGCACCCATAATGTTCTCAAACAAAATGGCAAGA
+CTAGGGAAAGGGTACATGTTCGAGAGTAAAAGAATGAAGATTCGAACACAAATACCAGCAGAAATGCTAG
+CAAGCATTGACCTGAAGTACTTCAATGAATCAACAAAGAAGAAAATTGAGAAAATAAGGCCTCTTCTAAT
+AGATGGCACAGCATCACTGAGTCCTGGGATGATGATGGGCATGTTCAACATGCTAAGTACGGTCTTGGGA
+GTCTCGATACTGAATCTTGGACAAAAGAAATACACCAAGACAATATACTGGTGGGATGGGCTCCAATCAT
+CCGACGATTTTGCTCTCATAGTGAATGCACCAAACCATGAGGGAATACAAGCAGGAGTGGACAGATTCTA
+CAGGACCTGCAAGTTAGTGGGAATCAACATGAGCAAAAAGAAGTCCTATATAAATAAGACAGGGACATTT
+GAATTCACAAGCTTTTTTTATCGCTATGGATTTGTGGCTAATTTTAGCATGGAGCTACCCAGCTTTGGAG
+TGTCTGGAGTAAATGAATCAGCTGACATGAGTATTGGAGTAACAGTGATAAAGAACAACATGATAAACAA
+TGACCTTGGACCTGCAACGGCCCAGATGGCTCTTCAATTGTTCATCAAAGACTACAGATACACATATAGG
+TGCCATAGGGGAGACACACAAATTCAGACGAGAAGATCATTTGAGTTAAAGAAGCTGTGGGATCAAACCC
+AATCAAAGGTAGGGCTATTAGTATCAGATGGAGGACCAAACTTATACAATATACGGAATCTTCACATTCC
+TGAAGTCTGCTTAAAATGGGAGCTAATGGATGATGATTATCGGGGAAGACTTTGTAATCCCCTGAATCCC
+TTTGTCAGTCATAAAGAGATTGATTCTGTAAACAATGCTGTGGTAATGCCAGCCCATGGTCCAGCCAAAA
+GCATGGAATATGATGCCGTTGCAACTACACATTCCTGGATTCCCAAGAGGAATCGTTCTATTCTCAACAC
+AAGCCAAAGGGGAATTCTTGAGGATGAACAGATGTACCAGAAGTGCTGCAATCTATTCGAGAAATTTTTC
+CCTAGCAGTTCATATAGGAGACCGGTTGGAATTTCTAGCATGGTGGAGGCCATGGTGTCTAGGGCCCGGA
+TTGATGCCAGGGTCGACTTCGAGTCTGGACGGATCAAGAAAGAAGAGTTCTCTGAGATCATGAAGATCTG
+TTCCACCATTGAAGAACTCAGACGGCAAAAATAA
+>H1N1_PB2
+ATGGAGAGAATAAAAGAACTGAGAGATCTAATGTCGCAGTCCCGCACTCGCGAGATACTCACTAAGACCA
+CTGTGGACCATATGGCCATAATCAAAAAGTACACATCAGGAAGGCAAGAGAAGAACCCCGCACTCAGAAT
+GAAGTGGATGATGGCAATGAGATACCCAATTACAGCAGACAAGAGAATAATGGACATGATTCCAGAGAGG
+AATGAACAAGGACAAACCCTCTGGAGCAAAACAAACGATGCTGGATCAGACCGAGTGATGGTATCACCTC
+TGGCCGTAACATGGTGGAATAGGAATGGCCCAACAACAAGTACAGTTCATTACCCTAAGGTATATAAAAC
+TTATTTCGAAAAGGTCGAAAGGTTGAAACATGGTACCTTCGGCCCTGTCCACTTCAGAAATCAAGTTAAA
+ATAAGGAGGAGAGTTGATACAAACCCTGGCCATGCAGATCTCAGTGCCAAGGAGGCACAGGATGTGATTA
+TGGAAGTTGTTTTCCCAAATGAAGTGGGGGCAAGAATACTGACATCAGAGTCACAGCTGGCAATAACAAA
+AGAGAAGAAAGAAGAGCTCCAGGATTGTAAAATTGCTCCCTTGATGGTGGCGTACATGCTAGAAAGAGAA
+TTGGTCCGTAAAACAAGGTTTCTCCCAGTAGCCGGCGGAACAGGCAGTGTTTATATTGAAGTGTTGCACT
+TAACCCAAGGGACGTGCTGGGAGCAGATGTACACTCCAGGAGGAGAAGTGAGAAATGATGATGTTGACCA
+AAGTTTGATTATCGCTGCTAGAAACATAGTAAGAAGAGCAGCAGTGTCAGCAGACCCATTAGCATCTCTC
+TTGGAAATGTGCCACAGCACACAGATTGGAGGAGTAAGGATGGTGGACATCCTTAGACAGAATCCAACTG
+AGGAACAAGCCGTAGACATATGCAAGGCAGCAATAGGGTTGAGGATTAGCTCATCTTTCAGTTTTGGTGG
+GTTCACTTTCAAAAGGACAAGCGGATCATCAGTCAAGAAAGAAGAAGAAGTGCTAACGGGCAACCTCCAA
+ACACTGAAAATAAGAGTACATGAAGGGTATGAAGAATTCACAATGGTTGGGAGAAGAGCAACAGCTATTC
+TCAGAAAGGCAACCAGGAGATTGATCCAGTTGATAGTAAGCGGGAGAGACGAGCAGTCAATTGCTGAGGC
+AATAATTGTGGCCATGGTATTCTCACAAGAGGATTGCATGATCAAGGCAGTTAGGGGCGATCTGAACTTT
+GTCAATAGGGCAAACCAGCGACTGAACCCCATGCACCAACTCTTGAGGCATTTCCAAAAAGATGCAAAAG
+TGCTTTTCCAGAACTGGGGAATTGAATCCATCGACAATGTGATGGGAATGATCGGAATACTGCCCGACAT
+GACCCCAAGCACGGAGATGTCGCTGAGAGGGATAAGAGTCAGCAAAATGGGAGTAGATGAATACTCCAGC
+ACGGAGAGAGTGGTAGTGAGTATTGACCGATTTTTAAGGGTTAGAGATCAAAGAGGGAACGTACTATTGT
+CTCCCGAAGAAGTCAGTGAAACGCAAGGAACTGAGAAGTTGACAATAACTTATTCGTCATCAATGATGTG
+GGAGATCAATGGCCCTGAGTCAGTGCTAGTCAACACTTATCAATGGATAATCAGGAACTGGGAAATTGTG
+AAAATTCAATGGTCACAAGATCCCACAATGTTATACAACAAAATGGAATTTGAACCATTTCAGTCTCTTG
+TCCCTAAGGCAACCAGAAGCCGGTACAGTGGATTCGTAAGGACACTGTTCCAGCAAATGCGGGATGTGCT
+TGGGACATTTGACACTGTCCAAATAATAAAACTTCTCCCCTTTGCTGCTGCTCCACCAGAACAGAGTAGG
+ATGCAATTTTCCTCATTGACTGTGAATGTGAGAGGATCAGGGTTGAGGATACTGGTAAGAGGCAATTCTC
+CAGTATTCAATTACAACAAGGCAACCAAACGACTTACAGTTCTTGGAAAGGATGCAGGTGCATTGACTGA
+AGATCCAGATGAAGGCACATCTGGGGTGGAGTCTGCTGTCCTGAGAGGATTTCTCATTTTGGGCAAAGAA
+GACAAGAGATATGGCCCAGCATTAAGCATCAATGAACTGAGCAATCTTGCAAAAGGAGAGAAGGCTAATG
+TGCTAATTGGGCAAGGGGACGTAGTGTTGGTAATGAAACGAAAACGGGACTCTAGCATACTTACTGACAG
+CCAGACAGCGACCAAAAGAATTCGGATGGCCATCAATTAG

environment.yml

@@ -1,5 +1,9 @@
 name: neat
 
+channels:
+  - bioconda
+  - conda-forge
+
 dependencies:
   - python==3.11.*
   - pip