nsarode

People

:bowtie:	😄 :smile:	😆 :laughing:
😊 :blush:	😃 :smiley:	☺️ :relaxed:
😏 :smirk:	😍 :heart_eyes:	😘 :kissing_heart:
😚 :kissing_closed_eyes:	😳 :flushed:	😌 :relieved:
😆 :satisfied:	😁 :grin:	😉 :wink:
😜 :stuck_out_tongue_winking_eye:	😝 :stuck_out_tongue_closed_eyes:	😀 :grinning:
😗 :kissing:	😙 :kissing_smiling_eyes:	😛 :stuck_out_tongue:

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Most used commands

# Get list of already set up environments
conda env list

# Create an environment with specified python version
conda create -n py36 python=3.6 anaconda

# Create environment without prompting for yes/no and quiet mode

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Version check

pd.__version__

Summary stats

df.describe()

Rows and column counts

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Generic

Cell operation shortcuts

❗ capitalization doesn't matter for these shortcuts

• b to add new cell below
• m change cell to markdown
• y change cell to code
• dd delete cell

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Reading

Open file for reading

f = open("somefile.txt", "r")
print(f.read()) # print entire file
print(f.read(4)) # print first 4 characters of the file

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# <author>Pieter Muller</author>
# <date>2012-11-14</date>

import sys
import sqlite3 as sqlite

tablesToIgnore = ["sqlite_sequence"]

outputFilename = None

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AWS-CLI way

First create a skeleton to edit

aws batch submit-job --generate-cli-skeleton > job.json

Edit the script as needed e.g. for the fetch-and-run job the final file FetchRunClijob.json looks like this

{

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Login

sudo $(aws ecr get-login --no-include-email --region us-east-1)

AWS Simple Storage Service (s3)

General

List buckets

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Extracting paired FASTQ read data from a BAM mapping file

Sometimes FASTQ data is aligned to a reference and stored as a BAM file, instead of the normal FASTQ read files. This is okay, because it is possible to recreate raw FASTQ files based on the BAM file. The following outlines this process. The useful software samtools and bedtools are both required.

From each bam, we need to extract:

1. reads that mapped properly as pairs
2. reads that didn’t map properly as pairs (both didn’t map, or one didn’t map)

For #1, the following command will work. This was taken from this webpage.

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REPLACEME: TITLE OF YOUR GRAPHGIST

Introduction