mossmatters

#!/usr/bin/env python

import argparse,sys,os,subprocess,shutil,errno
from Bio import SeqIO

helptext='''
This script is intended to use the results of a BLAST search of a transcriptome 
against a draft genome to conduct more specific exonerate alignments. Each transcript 
is paired with its genome scaffold hit using the BioPython Indexing feature.

benmarwick

# Adapted from https://stackoverflow.com/a/7267364/1036500 by Andrie de Vries

# This is it: theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5))

library(ggplot2)

td <- expand.grid(
  hjust=c(0, 0.5, 1),
  vjust=c(0, 0.5, 1),
  angle=c(0, 45, 90),

bomeara

chunks <- seq(from=0, to=1, length.out=7) # how finely we want to divide each univariate character

# 0.0000000 0.1666667 0.3333333 0.5000000 0.6666667 0.8333333 1.0000000

possible_states <- expand.grid(a=chunks, b=chunks, c=chunks) # all possible combinations (not adding up to 1). 
 #Doing just three chars here, you can add more: d=chunks, e=chunks....
sums <- apply(possible_states,1, sum)
possible_states <- possible_states[which(abs(sums-1)<0.00001),] # now limiting to those that add up to 1
rownames(possible_states) <- sequence(nrow(possible_states)) - 1 # state 0, 1, 2...