robsyme

##gff-version 3
##sequence-region scaffold_050 1 88013
scaffold_050	ACNFP_webapollo	gene	9950	10989	.	-	.	Name=AAF212BA0EDA71C39A7BB8B0E7CB232E;ID=AAF212BA0EDA71C39A7BB8B0E7CB232E
scaffold_050	ACNFP_webapollo	mRNA	9950	10989	.	-	.	Name=13090_t;Parent=AAF212BA0EDA71C39A7BB8B0E7CB232E;ID=3B13D87571355E374EF62FC9C6BB6307
scaffold_050	ACNFP_webapollo	CDS	10736	10989	.	-	0	Name=B875AE3EEF1D1FF4B90F85632ED90543;Parent=3B13D87571355E374EF62FC9C6BB6307;ID=B875AE3EEF1D1FF4B90F85632ED90543
scaffold_050	ACNFP_webapollo	CDS	10477	10678	.	-	2	Name=B875AE3EEF1D1FF4B90F85632ED90543;Parent=3B13D87571355E374EF62FC9C6BB6307;ID=B875AE3EEF1D1FF4B90F85632ED90543
scaffold_050	ACNFP_webapollo	CDS	9950	10417	.	-	0	Name=B875AE3EEF1D1FF4B90F85632ED90543;Parent=3B13D87571355E374EF62FC9C6BB6307;ID=B875AE3EEF1D1FF4B90F85632ED90543
scaffold_050	ACNFP_webapollo	exon	10736	10989	.	-	.	Name=DB4B25AB705E355774C61CC90FF5C9E7;Parent=3B13D87571355E374EF62FC9C6BB6307;ID=DB4B25AB705E355774C61CC90FF5C9E7
scaffold_050	ACNFP_webapollo	exon	9950	10417

robsyme

<text x="{{cmp.x1}}" y="20">{{cmp.name}}</text>

robsyme

FROM ubuntu:14.04
MAINTAINER Robert Syme <robsyme@gmail.com>

RUN sed 's/main$/main universe/' -i /etc/apt/sources.list
ENV DEBIAN_FRONTEND noninteractive
RUN apt-get update -qq
RUN apt-get upgrade -qqy

# Get wget
RUN apt-get install -qqy wget

robsyme

library(devtools)
#install_github("ropensci/rentrez")
library(rentrez)
library(tidyr)
library(ggplot2)

papers_by_year <- function(years, search_term){
  return(sapply(years, function(y) entrez_search(db="pubmed",term=paste('(', search_term, '[Title/Abstract]) AND ("Molecular plant-microbe interactions : MPMI"[Journal] OR ""[Journal] OR "Fungal genetics and biology : FG & B"[Journal])', sep = ""), mindate=y, maxdate=y, retmax=0)$count))
}

robsyme

/pbstore/groupfs/Curtin/bio-sci-02/WIP/PacBio-pea_pathogens.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/WIP/Af_1_new.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/me14_all_RNA_reads1.fa.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/me14_all_RNA_reads2.fa.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/trinity_Ar_me14_all_mink10_mcon150.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/me14_RNA/th2_me14v3_all.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/Ar_me14_v3assembly_140325/EVM_protein_analysis/me14_secretome_analysis.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_rabiei/Ar_me14/Ar_me14_v3assembly_140325/EVM_protein_analysis/me14_Pfam.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_lentis/Al_4/tRNA.tar.gz
/pbstore/groupfs/Curtin/bio-sci-02/A_lentis/Al_4/EVM_AL4.tar.gz

robsyme

=Slightly Safer Button Emergency Room=

Thanks to /u/BlueBlond for supplying the button. If you'd rather not trust that BlueBlond won't update the script to auto-click the button without your permission, this script offers a slightly safer option. The link is hard-coded to a specific version of the script in gist.

Link

robsyme

require "rubygems"
require "bio"

filepath = '/media/Store/data/sn15_genes/080611_sn15_aagi_gene.fas'

Bio::FlatFile.open(filepath) do |flatfile|
  flatfile.each do |entry|
    puts entry.entry_id
    puts entry.seq
    puts entry.seq.reverse_complement

robsyme

#!/bin/bash
echo "Starting script now..."
sleep 5m
vlc ~/Music/im_going_to_kill_you.mp3 --volume 1024
echo "Script done"

robsyme

%-3.fa: %-1.fa
	awk '/^>/ { getline s; if ($$3/($$2-$k+1)>=$c) \
		{ print $$0 "\n" s } }' $< \
		|ABYSS $v -k$k -l$l -e0 -o $@ -

robsyme

<BlastOutput>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_query-def>10000_g</Iteration_query-def>
      <Iteration_hits>
        <Hit>
          <Hit_def>hypothetical protein SNOG_01615</Hit_def>
           <Hit_hsps>
            <Hsp>
              <Hsp_score>1420</Hsp_score>