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Merge pull request #63 from pdimens/dev
stage release of version 0.9
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| name: Test Simulate Variants | ||
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| on: | ||
| push: | ||
| branches: | ||
| - 'dev' | ||
| paths: | ||
| - 'simulate**.smk' | ||
| - 'workflow/envs/harpy.yaml' | ||
| - '**helperfunctions.py' | ||
| - '**printfunctions.py' | ||
| - '**fileparsers.py' | ||
| - 'test/vcf/test.bcf' | ||
| - 'workflow/scripts/simuG.pl' | ||
| - '**__main__.py' | ||
|
|
||
| pull_request: | ||
| branches: | ||
| - 'dev' | ||
| paths: | ||
| - 'simulate**.smk' | ||
| - 'workflow/envs/harpy.yaml' | ||
| - '**helperfunctions.py' | ||
| - '**printfunctions.py' | ||
| - '**fileparsers.py' | ||
| - 'test/vcf/test.bcf' | ||
| - 'workflow/scripts/simuG.pl' | ||
| - '**__main__.py' | ||
|
|
||
| env: | ||
| CACHE_NUMBER: 0 # increase to reset cache manually | ||
|
|
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| jobs: | ||
| build: | ||
| name: test simulations | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: checkout | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 1 | ||
| - name: setup mamba | ||
| uses: mamba-org/setup-micromamba@v1 | ||
| env: | ||
| ACTIONS_STEP_DEBUG: true | ||
| with: | ||
| init-shell: bash | ||
| generate-run-shell: true | ||
| environment-file: workflow/envs/harpy.yaml | ||
| cache-environment: true | ||
| post-cleanup: 'all' | ||
| log-level: error | ||
| - name: Install harpy | ||
| shell: micromamba-shell {0} | ||
| run: | | ||
| python3 -m pip install --upgrade build && python3 -m build | ||
| pip install dist/*.whl | ||
| resources/buildforCI.sh | ||
| - name: simulate random snps/indels | ||
| shell: micromamba-shell {0} | ||
| run: | | ||
| harpy simulate snpindel --snp-count 10 --indel-count 10 -z 0.5 test/genome/genome.fasta.gz | ||
| harpy simulate snpindel --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/sim.snpindel.snp.hap1.vcf --indel-vcf Simulate/snpindel/sim.snpindel.indel.hap1.vcf test/genome/genome.fasta.gz | ||
| - name: simulate inversions | ||
| shell: micromamba-shell {0} | ||
| if: always() | ||
| run: | | ||
| harpy simulate inversion --count 10 -z 0.5 test/genome/genome.fasta.gz | ||
| harpy simulate inversion --prefix Simulate/invvcf --vcf Simulate/inversion/sim.inversion.hap1.vcf test/genome/genome.fasta.gz | ||
| - name: simulate cnv | ||
| shell: micromamba-shell {0} | ||
| if: always() | ||
| run: | | ||
| harpy simulate cnv --count 10 -z 0.5 test/genome/genome.fasta.gz | ||
| harpy simulate cnv --prefix Simulate/cnvvcf --vcf Simulate/cnv/sim.cnv.hap1.vcf test/genome/genome.fasta.gz | ||
| - name: simulate translocations | ||
| shell: micromamba-shell {0} | ||
| if: always() | ||
| run: | | ||
| harpy simulate translocation --count 10 -z 0.5 test/genome/genome.fasta.gz | ||
| harpy simulate translocation --prefix Simulate/transvcf --vcf Simulate/translocation/sim.translocation.hap1.vcf test/genome/genome.fasta.gz | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -8,6 +8,7 @@ Genome/ | |
| Align/ | ||
| SNP/ | ||
| SV/ | ||
| Simulate/ | ||
| Impute/ | ||
| Preflight/ | ||
| Phase/ | ||
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| #! /usr/bin/env python3 | ||
| import argparse | ||
| parser = argparse.ArgumentParser( | ||
| prog='makewindows.py', | ||
| description='Create a BED file of fixed intervals from a fasta.fai file (generated with samtools faidx). Nearly identical to bedtools makewindows, except the intervals are nonoverlapping.' | ||
| ) | ||
| parser.add_argument("-i", dest = "infile", required = True, type=str, metavar = "<input.fasta.fai>", help="input fasta.fai file") | ||
| parser.add_argument("-o", dest = "outfile", required = True, type=str, metavar = "<output.bed>", help="output BED file name") | ||
| parser.add_argument("-w", dest = "window", type=int, metavar = "<window_size>", default = "10000", help="interval size (default: %(default)s)") | ||
| args = parser.parse_args() | ||
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| with open(args.infile, "r") as fai: | ||
| outbed = open(args.outfile, "w") | ||
| while True: | ||
| # Get next line from file | ||
| line = fai.readline() | ||
| # if line is empty | ||
| # end of file is reached | ||
| if not line: | ||
| break | ||
| # split the line by tabs | ||
| lsplit = line.split("\t") | ||
| contig = lsplit[0] | ||
| c_len = int(lsplit[1]) | ||
| start = 1 | ||
| end = args.window | ||
| starts = [1] | ||
| ends = [args.window] | ||
| while end < c_len: | ||
| end = end + args.window if (end + args.window) < c_len else c_len | ||
| ends.append(end) | ||
| start += args.window | ||
| starts.append(start) | ||
|
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| # write to output file | ||
| for (startpos, endpos) in zip (starts,ends): | ||
| outbed.write(f"{contig}\t{startpos}\t{endpos}\n") | ||
| outbed.close() |
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