Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add pyrho genetic maps #572

Merged
merged 2 commits into from
Aug 1, 2020
Merged

Add pyrho genetic maps #572

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
9400a92
Add pyrho genetic maps
jeffspence Jul 31, 2020
d0f0596
Update __init__.py
jeffspence Aug 1, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
45 changes: 38 additions & 7 deletions stdpopsim/catalog/HomSap/__init__.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,6 +61,13 @@
author="The International HapMap Consortium",
)

_takahata1993 = stdpopsim.Citation(
doi="https://doi.org/10.1093/oxfordjournals.molbev.a039995",
year="1993",
author="Takahata",
reasons={stdpopsim.CiteReason.POP_SIZE}
)

_tian2019 = stdpopsim.Citation(
doi="https://doi.org/10.1016/j.ajhg.2019.09.012",
year="2019",
Expand All @@ -75,13 +82,6 @@
reasons={stdpopsim.CiteReason.GEN_TIME}
)

_takahata1993 = stdpopsim.Citation(
doi="https://doi.org/10.1093/oxfordjournals.molbev.a039995",
year="1993",
author="Takahata",
reasons={stdpopsim.CiteReason.POP_SIZE}
)

_chromosomes = []
for name, data in genome_data.data["chromosomes"].items():
_chromosomes.append(stdpopsim.Chromosome(
Expand Down Expand Up @@ -174,6 +174,37 @@
)
_species.add_genetic_map(_gm)

# 26 populations in 1000 Genomes
for pop in ["ACB", "ASW", "BEB", "CDX", "CEU", "CHB", "CHS", "CLM", "ESN",
"FIN", "GBR", "GIH", "GWD", "IBS", "ITU", "JPT", "KHV", "LWK",
"MSL", "MXL", "PEL", "PJL", "PUR", "STU", "TSI", "YRI"]:
_gm = stdpopsim.GeneticMap(
species=_species,
id="Pyrho{}_GRCh37".format(pop),
description="Pyrho population-specific map for {}".format(pop),
long_description="""
This genetic map was inferred using individuals from the {}
population from Phase 3 of the 1000 Genomes Project. Rates
were estimated using pyrho (https://github.com/popgenmethods/pyrho)
while using population-specific population size history estimates
obtained from smc++ (https://github.com/popgenmethods/smcpp).
Genetic maps are only available for the 22 autosomes.
See https://doi.org/10.1126/sciadv.aaw9206 for more
details.""".format(pop),
url=(
"https://stdpopsim.s3-us-west-2.amazonaws.com/genetic_maps/"
"HomSap/Pyrho{}_GRCh37.tar.gz".format(pop)),
file_pattern=(
"Pyrho{}_GRCh37_chr{{id}}.txt".format(pop)),
citations=[
stdpopsim.Citation(
Copy link
Member

@andrewkern andrewkern Jul 31, 2020 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

maybe pull this citation out of here and set it to _spence_song_2019 as with the other citations?

year=2019,
author="Spence and Song",
doi="https://doi.org/10.1126/sciadv.aaw9206",
reasons={stdpopsim.CiteReason.GEN_MAP})]
)
_species.add_genetic_map(_gm)


###########################################################
#
Expand Down