Usage: `hapmap = homo_sapiens.HapmapII_GRCh37()` (note the
parentheses).
The Phase II HapMap Genetic map (lifted over to GRCh37) used in
1000 Genomes. Please see the `README
<ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110106_recombination_hotspots/README_hapmapII_GRCh37_map>`_
for more details.
"""
url = ("http://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/"
"20110106_recombination_hotspots/"
"HapmapII_GRCh37_RecombinationHotspots.tar.gz")
file_pattern = "genetic_map_GRCh37_{name}.txt"
doi = "https://doi.org/10.1038/nature06258"
genetic_maps.register_genetic_map(HapmapII_GRCh37())
class Decode_2010_sex_averaged(genetic_maps.GeneticMap):
"""
Usage: `decode = homo_sapiens.Decode_2010()` (note the
parentheses).
Decode fine scale genetic map from Kong, A et al. Fine scale
recombination rate differences
between sexes, populations and individuals. Nature (28 October 2010).
(http://www.nature.com/nature/journal/v467/n7319/full/nature09525.html)
Please see https://www.decode.com/addendum/ for more details.
"""
url = ("http://sesame.uoregon.edu/~adkern/stdpopsim/decode/"
"decode_2010_sex-averaged_map.tar.gz")
class Salome2012(genetic_maps.GeneticMap):
"""
Genetic map from Salome 2012 averaged across population crosses.
Please see this repo for details on how this was done: https://github.com/
LohmuellerLab/arabidopsis_recomb_maps
"""
url = ("http://www.eeb.ucla.edu/Faculty/Lohmueller/data/"
"uploads/salome2012_maps.tar.gz")
file_pattern = "arab_{name}_map_loess.txt"
genetic_maps.register_genetic_map(Salome2012())
###########################################################
#
# Genome definition
#
###########################################################
# Data for length information based on:
# https://www.arabidopsis.org/portals/genAnnotation/
# gene_structural_annotation/agicomplete.jsp
# Lengths from TAIR 10 although its unclear what reference the genetic map used
# -- follow up on this with Salome 2012 authors
_chromosome_data = """\
chr1 30427671
# Genetic maps
#
###########################################################
class Comeron2012_dm6(genetic_maps.GeneticMap):
"""
Comeron et al. (2012) maps (lifted over to dm6) used in
Currently needs a readme as to the lift over, etc.
"""
url = ("http://sesame.uoregon.edu/~adkern/dmel_recombination_map/"
"comeron2012_maps.tar.gz")
file_pattern = "genetic_map_comeron2012_dm6_{name}.txt"
genetic_maps.register_genetic_map(Comeron2012_dm6())
###########################################################
#
# Genome definition
#
###########################################################
# List of chromosomes. Data for length information based on DM6,
# https://www.ncbi.nlm.nih.gov/genome/?term=drosophila+melanogaster.
# FIXME: add mean mutation and recombination rate data to this table.
_chromosome_data = """\
chrX 23542271
chr2L 23513712
chr2R 25286936
chr3L 28110227
Usage: `hapmap = homo_sapiens.HapmapII_GRCh37()` (note the
parentheses).
The Phase II HapMap Genetic map (lifted over to GRCh37) used in
1000 Genomes. Please see the `README
<ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20110106_recombination_hotspots/README_hapmapII_GRCh37_map>`_
for more details.
"""
url = (
"http://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/"
"20110106_recombination_hotspots/"
"HapmapII_GRCh37_RecombinationHotspots.tar.gz")
file_pattern = "genetic_map_GRCh37_{name}.txt"
genetic_maps.register_genetic_map(HapmapII_GRCh37())
###########################################################
#
# Genome definition
#
###########################################################
# List of chromosomes.
# FIXME: add mean mutation rate data to this table.
# Name Length mean_recombination_rate mean_mutation_rate
# length information can be found here
# <http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz>