peterdfields

#!/usr/bin/env sh

##
# This is script with usefull tips taken from:
#   https://github.com/mathiasbynens/dotfiles/blob/master/.osx
#
# install it:
#   curl -sL https://raw.github.com/gist/2108403/hack.sh | sh
#

peterdfields

import gzip
import csv
import argparse
import sys

parser = argparse.ArgumentParser(description="script to convert an all sites vcf to sweepfinder format. FASTA description will be the sample name in the VCF header.Only does one chromosome/region at a time.")
parser.add_argument("-v", "--vcf", action="store", required=True, help="Input VCF file. Should be a multisample vcf, though it should theoretically work with a single sample.")
parser.add_argument("-o", "--out", action="store", required=True, help="Output filename")
parser.add_argument("-c", "--chromosome", action="store", required=True, help="Chromosome to output. Should be something in the first column of the vcf.")
parser.add_argument("-g", "--gzip", action="store_true", required=False, help="Set if the VCF is gzipped.")

peterdfields

import gzip
import csv
import argparse
import sys

parser = argparse.ArgumentParser(description="script to convert an all sites vcf to FASTA format. FASTA description will be the sample name in the VCF header.Only does one chromosome/region at a time.")
parser.add_argument("-v", "--vcf", action="store", required=True, help="Input VCF file. Should be a multisample vcf, though it should theoretically work with a single sample.")
parser.add_argument("-o", "--out", action="store", required=True, help="Output filename")
parser.add_argument("-c", "--chromosome", action="store", required=True, help="Chromosome to output. Should be something in the first column of the vcf.")
parser.add_argument("-g", "--gzip", action="store_true", required=False, help="Set if the VCF is gzipped.")

peterdfields

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)