davetang

#!/usr/bin/env bash

set -euo pipefail

sudo apt-get update
sudo apt-get install -y \
    ca-certificates \
    curl \
    gnupg \
    lsb-release \

davetang

#!/usr/bin/env bash

set -euo pipefail

usage() {
   >&2 echo "Usage: $0 [ -l search_list ] [ -f file_to_grep ] [ -n split_num ] [ -p num_threads ]"
   exit 1
}

num_param=4

davetang

Keybase proof

I hereby claim:

• I am davetang on github.
• I am davetang (https://keybase.io/davetang) on keybase.
• I have a public key ASD791k70QUxQTjAu2NfaNCa4dhCxY0EnzWk-AT0uqFOSQo

To claim this, I am signing this object:

davetang

#!/bin/bash

if type -P gemini > /dev/null

   then
      for SEVERITY in HIGH MED LOW; do
         gemini query -q "select impact_so, count(impact_so) from variants where impact_severity == \"$SEVERITY\" group by impact_so order by count(impact_so)" --header *.db > $SEVERITY.tsv
         plot_gemini.R $SEVERITY.tsv
         rm -f $SEVERITY.tsv
      done

davetang

#!/usr/bin/env Rscript
#
# Usage: plot_gemini.R <file.tsv>
#

my_required <- c('ggplot2', 'reshape2', 'ggthemes')
for (my_package in my_required){
   if(my_package %in% rownames(installed.packages()) == FALSE){
      stop(paste("Please install", my_package, "first")) 
   }

davetang

#!/usr/bin/env perl

# Script to output names and synonyms of HPO terms

use strict;
use warnings;

my $usage = "Usage: $0 <HPO term> [HPO terms]\n";

if (scalar(@ARGV) == 0){

davetang

#!/usr/bin/env perl

# Strings (the query) present on each line of a file are matched to Human Phenotype Ontology (HPO) terms (the subject)
# If a direct match between the query and subject could not be found, a global alignment is performed
# Alignments will only take place between queries and subjects that are not longer than each 
# other by a length of 5 characters (including spaces)
# For example, 'short' and 'microphones' differ by a length of 6 and will not be compared
# The terms 'short' and 'computer' will be aligned because they differ by a length of 3
# Change $threshold if you want to change the length difference threshold

davetang

#!/usr/bin/env perl

#
# Reads a tab-delimited file with column and row names
# sums the rows and columns and outputs a tab-delimited
# file with an extra row and column for the sums
#

use strict;
use warnings;

davetang

#!/usr/bin/env perl

# Takes a fasta file as input and randomly mutates bases

use strict;
use warnings;

my $usage = "Usage: $0 <infile.fa> <mutation percent> <seed>\n";
my $infile = shift or die $usage;
my $mutation = shift or die $usage;

davetang

#!/usr/bin/env perl

# Simple script that takes an input fasta sequence
# and generates paired end reads

use strict;
use warnings;

my $usage = "Usage: $0 <infile.fa> <read length> <number of pairs> <inner mate distance> <seed>\n";
my $fasta = shift or die $usage;