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library(lubridate)
library(dplyr)

#fake data as an example, just 4 ranodm dates in the last month
set.seed(123)
fake_data_a <- data.frame(date = today() - sample(30,4), value_a=rnorm(4))
fake_data_b <- data.frame(date = today() - sample(30,4), value_b=rnorm(4))

#find all the dates in the window dfeine by fake_data_a
all_dates <- data.frame(date = seq(min(fake_data_a$date), max(fake_data_a$date), by=1))

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license: cc-by-4.0
height: 1800
scrolling: no
border: yes

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def base_consensus(alignment, base_index):
    """ """
    # get the bases at this position, store in case we want to come back 
    # and assign the first one as th winner
    #n_seqs = len(alignment)
    bases = [r[base_index].upper() for r in alignment]
    base_c = Counter(bases)
    max_count = max(base_c.values())
    most_common_base  = [b for b in base_c.items() if b[1] == max_count]
    if len(most_common_base) == 1:

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$include /etc/inputrc

"\e[A":history-search-backward
"\e[B":history-search-forward


export HISTSIZE=1000000
export HISTFILESIZE=1000000000

export HISTIGNORE='pwd:ls:history:'

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from collections import defaultdict
from Bio import SeqIO

class Orthologs:
    def __init__(self, ortho_file, seq_map_file):       
        """Store information on orthologs from another of strains """

        self.ortholog_map = defaultdict(lambda: defaultdict(list))
        with open(ortho_file) as infile:

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tail cov.tsv -n1  | cut -f1,2 > spp.genome
bedtools makewindows -g spp.genome  -w 1000 > spp_1kw.bed
awk -v OFS='\t' '{print $1,($2 -1),$2,$3 }' cov.tsv  > cov.bed
bedtools map -a spp_1kw.bed -b cov.bed  -c 4 -o mean

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sample_half_disk <- function(n,radius) {
   prop_radius <- runif(n)
   angles <- runif(n,0,360)
   data.frame( x= sqrt(prop_radius) * cos(angles) * radius,
               y = -abs(sqrt(prop_radius) * sin(angles) * radius))
}

plot(sample_half_disk(1e4,300))

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.one_chrom_outline <- function(chrom_name, len, offset, width, centro_s, centro_e, notch_prop=0.6){
    one_side <- c(0, centro_s-offset, (centro_s + centro_e)/2, centro_e+offset, len)
    wd = width/2
    data.frame(
      chrom = chrom_name,
      x = c(one_side, rev(one_side), 0),
      y = c(wd, wd, notch_prop * wd, wd, wd, -wd, -wd, -notch_prop * wd, -wd, -wd, wd)
      )    

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```
---
name: rotl-paper-published
layout: post
title: "rotl paper published"
date: 2016-18-02
authors: 
  - name: Francois Michonneau
    url: http://francoismichonneau.net/
  - name: Joseph Brown