ctokheim

# SE
cat SE.MATS.ReadsOnTargetAndJunctionCounts.txt | awk -F"\t" '{if($5=="+") print $5 $4 ":" $6 "-" $7 "," $5 $4 ":" $8 "-" $9 "," $5 $4 ":" $10 "-" $11; else print $5 $4 ":" $6 "-" $7 "," $5 $4 ":" $10 "-" $11 "," $5 $4 ":" $8 "-" $9;}' | tail -n +2 > se.txt

# MXE
cat MXE.MATS.ReadsOnTargetAndJunctionCounts.txt | awk -F"\t" '{if($5=="+") print $5 $4 ":" $6 "-" $7 "," $5 $4 ":" $10 "-" $11 "," $5 $4 ":" $12 "-" $13; else print $5 $4 ":" $6 "-" $7 "," $5 $4 ":" $12 "-" $13 "," $5 $4 ":" $10 "-" $11 }' | tail -n +2  > mxe.txt

ctokheim

# Old versions of GNU libc can create problems for running binaries on linux.
# In general GNU libc is backward compatible but in no way is 
# "forward" compatible. This means when creating binaries for applications,
# like python with pyinstaller, you need to use the oldest version of GNU libc
# as possible. To check the version, use the following command:
ldd --version

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#!/bin/bash

#########################################
# Installing python and necessary packages
# locally. This script will install python
# into the ~/local/bin directory and install
# numpy + scipy
#########################################

# installing python 2.7.3

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#!/bin/bash

# Script for installing tmux on systems where you don't have root access.
# tmux will be installed in $HOME/local/bin.
# It's assumed that wget and a C/C++ compiler are installed.
# PATH variable will need to be updated with $HOME/local/bin and the
# LD_LIBRARY_PATH variable will need $HOME/local/lib

# exit on error
set -e

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# if get recieve.denyCurrentBranch error try to pull from
# the repository instead of pushing. Alternatively just
# switch to a tmp branch.

# Permanently going back to previous commit
git reset --hard 123abc

# undo adding a file to be staged for commit
git reset myfile

ctokheim

import pandas as pd
import numpy as np

# read df from delimited file
df = pd.read_csv('filename.txt', sep='\t')

# force printing out of dataframe
print df.to_string()

# apply a function to column/row

ctokheim

Sublime Text 2 – Useful Shortcuts (PC)

Loosely ordered with the commands I use most towards the top. Sublime also offer full documentation.

Editing

Ctrl+C	copy current line (if no selection)
Ctrl+X	cut current line (if no selection)
Ctrl+⇧+K	delete line
Ctrl+↩	insert line after

ctokheim

# run command on certain files in a directory
for file in ./myDir/*.abc
do
  cmd [options] $file > output.txt
done

# run command using integer ranges
for i in {1..5}
do
   echo "Welcome $i times"

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Overview

UCSC's track hubs allow multiple wig files to be displayed in a single custom track. Thus possibly overlaying multiple types of data or displaying strand specific read depth. Individual sub-tracks within a custom track can then be toggled on/off.

Getting Started

The official documentation of UCSC's track hubs can be found at http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html.

ctokheim

# sum a column
cat your_file.txt | awk '{sum+=$5} END {print sum}'

# use specific delimiters
cat your_file.txt | awk -F" " '{OFS="\t";}{print $1, $2-1, $3-1, $5}'

# grab certain lines in a file
cat your_file.txt | awk 'FNR==10'