disulfidebond

Overview

This gist details how to create or restore a disk image in Mac OSX. There are three methods that are described: Carbon Copy Cloner, Disk Utility, and CommandLine.

• Disclaimer:
  • I have no financial incentives to https://bombich.com or Apple.
  • Always make a backup of your data, and make 2 separate backups before trying something new.
  • The following steps have been tested and are a summary of my personal recommendations, but should be used at your own risk.
  • If there is a chance of imminent data loss, contact a professional for assistance, and do not rely on a random person from the Internet for help.

Method 1: Carbon Copy Cloner (CCC)

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#!/bin/sh

date
# outputs Fri Jan 25 12:10:33 CST 2019

# alternative: add to bash_profile
timestamp() {
        date +"%T"
}

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import time
import datetime

# credit: squiguy https://stackoverflow.com/a/13891070
t_stamp = time.time()

t_stamp_string = datetime.datetime.fromtimestamp(t_stamp).strftime('%Y-%m-%d %H:%M:%S')
# output: 2019-01-25 12:06:02
t_stamp_string = datetime.datetime.fromtimestamp(t_stamp).strftime('%Y.%m.%d.%H.%M.%S')
# output: 2019.01.25.12.07.16

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Unlock Keychain

• Explanation: this can be used to remotely (or within a Terminal session) to unlock keychain
• Requirements/Restrictions:
  • You must know the keychain password
  • This is confirmed to work on Mac OSX High Sierra, but may have different usage on other Mac OSX versions (Sierra, Mojave, etc)
• Cautions/Warnings:

  • This will unlock your keychain, which is a potential security risk that you may not want to happen.

    # command to use in Bash, will prompt for the password
    

If no keychain is specified, then the default will be used

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Description of Workflow

Step 3: Create a fasta file of exons that extends the window for mapping reads N base pairs in both directions, where N == the number of base pairs the for the sequencing length. For Illumina, this is usually 75 or 150.

• Required parameters:
  • ntype -> the type of input, possible options are:
    • rna -> indicates that the input sequenced read data is from rna/cDNA (mutually exclusive with dna)
    • dna -> indicates that the input sequenced read data is from dna (mutually exclusive with rna, do not enter dna for cDNA data)
  • filteredfile -> the file containing the input sequenced reads that will be used. Must be in MHC.dat format
• Other parameters:
• flength -> the length of padding for the reads, the default is 75

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Description of Workflow

Step 2: Use python file to parse the filtered output from part 1 (most likely the file named 'parsed_mhc_output.txt'). The python script uses argparse(), so it can be called from the commandline with one of the following options, but note that output is to STDOUT, so it will need to be redirected to a file.

• exonList -> a text file with a comma separated list of exons

• fastaExonList -> a fasta formatted list of exons

• mergedFastaList -> a fasta formatted list of cDNA sequences

            #!/usr/bin/python3
            import argparse
  

import time

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Description of Workflow

Step 1. download MHC dataset from IPD. It will have the file extension ".dat", however it can be viewed/edited as a text file. Note that it is very large, so opening it in Atom, BBEdit, or similar text editors/IDE is strongly discouraged.

A preview of this dataset is available here:

                login$ head -n 100 MHC_dat.txt 
                ID   NHP00001
                XX   

DT 15/07/2008 (Release)

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#!/bin/sh

echo 'WARNING!!  THIS SETUP IS NOT INTENDED'
echo 'FOR A PRODUCTION ENVIRONMENT IN ANY CAPACITY!!!'
sleep 3

STARTDIR=$(PWD)
mkdir installspacepg
cd ./installspacepg

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# standard bash profile
# segments borrowed from stephnell on Github

# PATH
# You need to have this line of code.  It sets up your Bash $PATH, which is the file that directs Bash how to run programs
# the syntax is:
# export -> this tells Bash to set up PATH with the following values:
# PATH= -> this tells Bash to assign whatever your type next to the PATH variable
# $PATH: -> this is *very* important--it tells Bash not to throw away what was in your PATH already, 
#  #  but to append to it instead.  If you leave this out, your Bash shell may not work!