for del_size in 10 30 50 70 90 150 300 600
do
chr=17
start_pos=4126000
read_length=100
ens_url="http://grch37.rest.ensembl.org/sequence/region/human/"
qual=$(python -c "print 'A'*${read_length}")
(
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
color_grep_file() { | |
COLOR_CMD="cat $1" | |
echo $COLOR_CMD | |
local i=31; | |
while read line; do | |
echo $line | |
COLOR_CMD="$COLOR_CMD | GREP_COLOR='01;$i' grep --color=always -E '$line|$'" | |
i=$(( $i + 1 )) | |
done < $2 | |
COLOR_CMD="$COLOR_CMD | less -RS" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
for row in $(cat nucmer.coords | awk -v OFS=, '{if ($10 == 100.00 && $11 == 100.00 && $7 == 100.00 && $12 != $13) {print $12,$13}}') | |
do | |
echo $row | tr ',' '\n' | sort | tr '\n' ',' | sed 's/,$//' | |
echo | |
done | cut -d, -f2 | sort -u > duplicatecontigs.txt |
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
/** | |
* Python-like string format function | |
* @param {String} str - Template string. | |
* @param {Object} data - Data to insert strings from. | |
* @returns {String} | |
*/ | |
var format = function(str, data) { | |
var re = /{([^{}]+)}/g; | |
return str.replace(/{([^{}]+)}/g, function(match, val) { |
This file has been truncated, but you can view the full file.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
<!DOCTYPE html> | |
<html lang="en"> | |
<head> | |
<meta charset="utf-8"> | |
<title>Bokeh Plot</title> | |
<style> | |
/* BEGIN /Users/debruiji/anaconda/lib/python2.7/site-packages/bokeh/server/static/css/bokeh.min.css */ | |
.bk-bs-container{margin-right:auto;margin-left:auto;padding-left:15px;padding-right:15px}@media(min-width:768px){.bk-bs-container{width:750px}}@media(min-width:992px){.bk-bs-container{width:970px}}@media(min-width:1200px){.bk-bs-container{width:1170px}}.bk-bs-container-fluid{margin-right:auto;margin-left:auto;padding-left:15px;padding-right:15px}.bk-bs-row{margin-left:-15px;margin-right:-15px}.bk-bs-col-xs-1,.bk-bs-col-sm-1,.bk-bs-col-md-1,.bk-bs-col-lg-1,.bk-bs-col-xs-2,.bk-bs-col-sm-2,.bk-bs-col-md-2,.bk-bs-col-lg-2,.bk-bs-col-xs-3,.bk-bs-col-sm-3,.bk-bs-col-md-3,.bk-bs-col-lg-3,.bk-bs-col-xs-4,.bk-bs-col-sm-4,.bk-bs-col-md-4,.bk-bs-col-lg-4,.bk-bs-col-xs-5,.bk-bs-col-sm-5,.bk-bs-col-md-5,.bk-bs-col-lg-5,.bk-bs-col-xs-6,.bk-bs-col-sm-6,.bk-bs-col-md-6,.bk-bs-col-lg-6,.bk |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/sh | |
rightpath() { | |
path="" | |
for d in `readlink -f $1 | tr / " "` | |
do | |
path="$path/$d" | |
stat -c "%A %a %U %G %n" $path | |
done | column -t | |
} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/sh | |
parallel lib1={}';' \ | |
lib2='$('echo {} '|' sed s/_1.fastq.gz/_2.fastq.gz/');' \ | |
base='$('basename {} _1.fastq.gz');' \ | |
sickle pe -f '$lib1' -r '$lib2' -t sanger \ | |
-o '$base'.sickle.pe1.fastq \ | |
-p '$base'.sickle.pe2.fastq \ | |
-s '$base'.sickle.se.fastq \ | |
::: /proj/b2010008/INBOX/A.Andersson_13_06/*/*/*_1.fastq.gz |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/usr/bin/env ruby | |
grep = `git grep -n #{ARGV[0]} #{ARGV[1]}` | |
puts "\n-----------------------------------------------------------" | |
puts "GREP RESULT" | |
puts '-----------------------------------------------------------' | |
puts grep | |
files = grep.scan /.*\:\d+/ |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
#!/bin/bash | |
DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) | |
export PORTAL_HOME=$DIR |