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docs: better showcase example files and their locations in simgenotype #166

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Jan 27, 2023
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docs: better showcase example files and their locations in simgenotype #166

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51b8088
Updated simgenotype --model docs to send people to file format
mlamkin7 Jan 25, 2023
fc94569
Update example file documentation for simgenotype
mlamkin7 Jan 27, 2023
7131ffc
move comma
aryarm Jan 27, 2023
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5 changes: 5 additions & 0 deletions docs/commands/simgenotype.rst
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Expand Up @@ -73,6 +73,11 @@ If speed is important, it's generally faster to use PGEN files than VCFs.
--pop_field \
--out tests/data/example_simgenotype.pgen

Example model files found in `haptools/example-files/models/ <https://github.com/CAST-genomics/haptools/tree/main/example-files/models>`_ and `haptools/tests/data/ <https://github.com/CAST-genomics/haptools/tree/main/tests/data>`_.
Example map files found in `haptools/tests/data/map/ <https://github.com/CAST-genomics/haptools/tree/main/tests/data/map>`_.
Example ref_vcf file can be found `haptools/tests/data/outvcf_test.vcf <https://github.com/CAST-genomics/haptools/blob/main/tests/data/outvcf_test.vcf>`_.
Example sample_info files found in `haptools/example-files/ <https://github.com/CAST-genomics/haptools/tree/main/example-files>`_ and `haptools/tests/data/outvcf_info.tab <https://github.com/CAST-genomics/haptools/blob/main/tests/data/outvcf_info.tab>`_.


Detailed Usage
~~~~~~~~~~~~~~
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5 changes: 5 additions & 0 deletions docs/formats/models.rst
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Expand Up @@ -40,3 +40,8 @@ Example pulse event model.dat file
4 1 0 0

Simulating 40 samples for 4 generations in this case implies the first generation has population freqs ``Admixed=0, CEU=0.2, YRI=0.8`` the second generation is purely admixed, the third has an event where a pure CEU population is introduced again at freqs ``Admixed=0.5, CEU=0.5, YRI=0`` and finally we end with pure admixture.

More Example files
------------------
We have generated example model files that simulate current population structures within different populations in America as well as the Caribbean that can be found in the haptools repository here: `haptools/example-files/models/ <https://github.com/CAST-genomics/haptools/tree/main/example-files/models>`_
There are additional example model files that can be found in the haptools repository under `haptools/tests/data/ <https://github.com/CAST-genomics/haptools/tree/main/tests/data>`_
5 changes: 4 additions & 1 deletion haptools/__main__.py
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Expand Up @@ -88,7 +88,10 @@ def karyogram(bp, sample, out, title, centromeres, colors, verbosity):
"--model",
type=str,
required=True,
help="Admixture model in .dat format. See docs for info.",
help=(
"Admixture model in .dat format. See File Formats under simgenotype in the "
"docs for complete info."
),
)
@click.option(
"--mapdir",
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