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mlamkin7 merged 6 commits into from
Jun 30, 2022
Merged

Feat/vcf output #57

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09a757c
Updated Example in __main__.py
mlamkin7 Jun 30, 2022
8f91078
Update simgenotype.md
mlamkin7 Jun 30, 2022
8e95499
Update simgenotype.md
mlamkin7 Jun 30, 2022
2b5e501
Update simgenotype.md
mlamkin7 Jun 30, 2022
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Update simgenotype.md
mlamkin7 Jun 30, 2022
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14 changes: 7 additions & 7 deletions docs/commands/simgenotype.md
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Expand Up @@ -77,11 +77,11 @@ Sample Header 2

Example Command
```
haptools simgenotype
--invcf 1000Genomes.vcf.gz \
--sample_info /path/to/sampleinfo.csv \
--model /path/to/model/file.dat \
--map /path/to/plink/file/ \
--chroms 7,8,9,10,21,22,X \
--out /path/to/output
haptools simgenotype \
--model ./tests/data/outvcf_gen.dat \
--mapdir ./tests/data/map/ \
--chroms 1,2 \
--invcf ./tests/data/outvcf_test.vcf \
--sample_info ./tests/data/outvcf_info.tab \
--out ./tests/data/example_simgenotype
```
11 changes: 7 additions & 4 deletions haptools/__main__.py
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Expand Up @@ -67,13 +67,16 @@ def karyogram(bp, sample, out, title, centromeres, colors):
"describing the populations in the header of the model file.", required=True)
def simgenotype(invcf, sample_info, model, mapdir, out, popsize, seed, chroms):
"""
Simulate admixed genomes under a pre-defined model
Simulate admixed genomes under a pre-defined model.

Example:
haptools simgenotype \
--model tests/data/dat_files/AFR_south_carolina.dat \
--mapdir map/ \
--out test
--model ./tests/data/outvcf_gen.dat \
--mapdir ./tests/map/ \
--chroms 1,2 \
--invcf ./tests/data/outvcf_test.vcf \
--sampleinfo ./tests/data/outvcf_info.tab \
--out ./tests/data/example_simgenotype
"""
from .sim_genotype import simulate_gt, write_breakpoints, output_vcf, validate_params
chroms = chroms.split(',')
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