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#!/usr/bin/python | |
# Run KING to generate sample QC and IBD summary stats | |
# ./king_1.9 -b <data>.bed --bysample --prefix <prefix_for_output> | |
# ./king_1.9 -b <data>.bed --kinship --related --degree 2 --prefix <prefix_for_output> | |
# | |
# Run this script to create a list of exclusions (member of pair with least data will be excluded) | |
# python king.py --prefix <prefix_for_output> --out <output_file_name> | |
# Add error if no samples in kinship file. |
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#!/usr/bin/env python | |
# Author: Guillaume Bouvier -- guillaume.bouvier@pasteur.fr | |
# https://research.pasteur.fr/en/member/guillaume-bouvier/ | |
# 2016-08-26 13:20:35 (UTC+0200) | |
# DSSP_SECONCARY.PY | |
# Trajectories of Secondary Structure by DSSP | |
# The keys [" ","B","E","G","H","I","T","S"] |
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""" | |
C-alpha test for rare variants. Copied from AssotesteR | |
Only reports the permutation p-value, not the asymptotic | |
This also wraps all of the functions in R's AssotesteR using | |
rpy2. Any function available in AssotesteR, e.g. CALPHA is | |
availailable here has r_calpha(). | |
The args are always | |
casecon: a list of 0's, 1's indicating case/control status |