adomingues

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adomingues

#!/usr/bin/env bash
# make_rRNA.sh
# Kamil Slowikowski
# Created: December 12, 2014
# Original: https://gist.github.com/slowkow/b11c28796508f03cdf4b
# Modified: January 22, 2014 
# António Domingues 
# Added arguments - easier to run and choose species
# rRNA coordinates can be in Bed format

adomingues

bedtools bamtofastq -i $bam -fq temp.fq
awk '{if(NR%4==1) {printf(">%s\n",substr($0,2));} else if(NR%4==2) print;}' temp.fq > ${bam/.bam/.fa}
rm temp.fp

adomingues

#install.packages(c("wordcloud","tm"),repos="http://cran.r-project.org")
library("wordcloud")
library("tm")

message <- c(
   rep("Good", 10),
   rep("Luck", 9),
   rep("Eyebrow", 3),
   rep("Tatra Tea", 4),
   rep("Sächsische Schweiz‎", 3),

adomingues

swatch <- function(x) {
  # x: a vector of colours (hex, numeric, or string)
  par(mai=c(0.2, max(strwidth(x, "inch") + 0.4, na.rm = TRUE), 0.2, 0.4))
  barplot(rep(1, length(x)), col=rev(x), space = 0.1, axes=FALSE, 
          names.arg=rev(x), cex.names=0.8, horiz=T, las=1)  
}
 
# Example:
# swatch(colours()[1:10])
# swatch(iwanthue(5))

adomingues

# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

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# Multiple plot function
#
# ggplot objects can be passed in ..., or to plotlist (as a list of ggplot objects)
# - cols:   Number of columns in layout
# - layout: A matrix specifying the layout. If present, 'cols' is ignored.
#
# If the layout is something like matrix(c(1,2,3,3), nrow=2, byrow=TRUE),
# then plot 1 will go in the upper left, 2 will go in the upper right, and
# 3 will go all the way across the bottom.
#

adomingues

### My favourite ggplot2 themes, always accessible ###
## just source this gist from any project ##


#####################################################################################

# Noam's default ggplot2 styling #####
# Source: https://github.com/noamross/noamtools/blob/master/R/theme_nr.R
theme_nr <-theme(text=element_text(family="Helvetica", size=14),
                 panel.grid.major.x=element_blank(),

adomingues

@SQ	SN:chrM	LN:16571
@SQ	SN:chr1	LN:249250621
@SQ	SN:chr2	LN:243199373
@SQ	SN:chr3	LN:198022430
@SQ	SN:chr4	LN:191154276
@SQ	SN:chr5	LN:180915260
@SQ	SN:chr6	LN:171115067
@SQ	SN:chr7	LN:159138663
@SQ	SN:chr8	LN:146364022
@SQ	SN:chr9	LN:141213431

adomingues

# A function (borrowed from the Sleuth documentation) for connecting Ensembl transcript names to common gene names
convert_tx_to_gene <- function(dat="drerio_gene_ensembl"){
    mart <- biomaRt::useMart(
        biomart = "ensembl",
        dataset = dat
    )
    t2g <- biomaRt::getBM(
        attributes = c("ensembl_transcript_id", "ensembl_gene_id", "external_gene_name"),
        mart = mart