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-- [[ Cheatsheet for LUA from http://www.newthinktank.com/2015/06/learn-lua-one-video/]] | |
-- Prints to the screen (Can end with semicolon) | |
print("Hello World") | |
--[[ | |
Multiline comment | |
]] | |
-- Variable names can't start with a number, but can contain letters, numbers |
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import pandas as pd | |
# fix SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Either of following | |
pd.options.mode.chained_assignment = None # default='warn' | |
df.is_copy = False | |
# read big csv | |
df = pd.read_csv(FILE_PATH, sep='\t', comment = '#', chunksize=1000, \ | |
low_memory=False, iterator = True, compression='gzip') |
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https://asia.ensembl.org/info/docs/tools/vep/script/vep_options.html | |
# Instructions for installing and running new VEP | |
## 1. Install new version of VEP: | |
git clone https://github.com/Ensembl/ensembl-vep.git | |
cd ensembl-vep | |
perl INSTALL.pl | |
## 2. Install merged cache |
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# -*- coding: utf-8 -*- | |
""" | |
Created on Mon Mar 5 14:21:42 2018 | |
@author: nilesh-tawari | |
email: tawari.nilesh@gmail.com | |
GitHub: https://github.com/nilesh-tawari | |
""" | |
from __future__ import print_function | |
import os |
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#!/usr/bin/env Rscript | |
################################################ | |
################################################ | |
## REQUIREMENTS ## | |
################################################ | |
################################################ | |
## DIFFERENTIAL ANALYSIS, SCATTERPLOTS AND PCA FOR SAMPLES IN FEATURECOUNTS FILE | |
## - FIRST SIX COLUMNS OF FEATURECOUNTS_FILE SHOULD BE INTERVAL INFO. REMAINDER OF COLUMNS SHOULD BE SAMPLES-SPECIFIC COUNTS. |
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# Create git repository and push to remote | |
cd workspace/Clinical_genomics_framework/ | |
git init | |
git add . | |
git commit -m "Clinical genomics framework" | |
echo "# Clinical_genomics_framework" >> README.md | |
git add README.md | |
git commit -m "Readme file" | |
Create a repo online using browser then push local to remote |
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#!/bin/bash | |
# $1 is PATH | |
args=("$@") | |
input_dir=${args[0]} | |
output_dir=${args[1]} | |
main() { | |
set -e -x -o pipefail | |
# get R1 | |
declare -a fastq1=($(ls -d $input_dir/*R1*.fastq.gz)) #($(ls *_R1_001.fastq.gz)) |
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## RNA-seq analysis with DESeq2 | |
## Stephen Turner, @genetics_blog | |
# RNA-seq data from GSE52202 | |
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with | |
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl") | |
# Import & pre-process ---------------------------------------------------- | |
# Import data from featureCounts |
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# -*- coding: utf-8 -*- | |
""" | |
Created on Tue Mar 13 09:40:36 2018 | |
@author: rameshtn | |
""" | |
from __future__ import print_function | |
import os | |
import argparse |
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# Deploy a python package on DNAnexus | |
## Step 1: find installation path of module | |
python | |
import imp | |
imp.find_module("pandas") | |
## Step 2: copy module and put in tarball | |
cp -r /mnt/software/unstowable/anaconda/lib/python2.7/site-packages/pandas . |
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