carlosp420

import json
import yaml


def parse_recipe(recipe, all_ingredients):
    for recipe_name, ingredients in recipe.items():
        for ingredient in ingredients:
            ingredient_name, amount, unit = ingredient
            try:
                all_ingredients[ingredient_name]['amount'] += amount

carlosp420

nosetests --verbosity 2 --with-doctest --with-coverage --cover-html -w Tests --cover-package Bio

carlosp420

#!/usr/bin/perl -w

#this script converts a tree ouput from TNT to NEXUS (1 tree per file)
# Carlos Peña 2011-03-16

use strict;
use Bio::TreeIO;
        my $usage = "script.pl INFILE OUTFILE\n";
        my $infile = shift or die $usage;
        my $outfile = shift or die $usage;

carlosp420

:%s/^/\=line('.')/

carlosp420

# convert marianna's files into bash commmand
sed 's/\(^[0-9]\+\),\(.\+\),.\+\*\(.\+\)/\3\*\1-\2/g' < Genus.csv > Genus.sh

# first part
sed  "s/^/sed -i 's\//g" < Genus.sh

# half
sed  "s/*/\//g" < Genu.sh

# last

carlosp420

cat bad_ids.csv | grep Agrilus   | awk -F ' ' '{print $3 " " $4  "*" $0}' | sort  > Agrilus.csv

carlosp420

view:
    http://localhost:5984/euptychiina/_design/references/_view/by_time

lucene:
    http://localhost:5984/euptychiina/_fti/_design/lucene/by_author?q=Pe*

carlosp420

##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)

carlosp420

pygmentize -O noclasses,style=emacs  -o a.html a.R

carlosp420

taken from: http://www.robertlanfear.com/partitionfinder/news/

Models in PartitionFinder and how to set them up in BEAST/BEAUti

JC:  in Beauti use the GTR with base frequences set to All equal and turn off all operators for parameters.
F81: in BEAUti use the GTR and turn off all operators for parameters
K80: in BEAUti this is “HKY” with “base frequencies” set to “All Equal”
TrNef: in BEAUti this is “TN93” with “base frequencies” set to “All Equal”
SYM: in BEAUti this is “GTR” with “base frequencies” set to “All Equal”
HKY: in BEAUti this is “HKY” with “base frequencies” set to “estimated”