| command | description |
|---|---|
| ctrl + a | Goto BEGINNING of command line |
Ayton Meintjes ameintjes
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
| # Last updated May, 2024 for Apple silicon Macs | |
| # Install Homebrew if you don't already have it: https://brew.sh | |
| # install nano from homebrew | |
| brew install nano nanorc | |
| # update your nanorc file | |
| echo 'include "'"$(brew --cellar nano)"'/*/share/nano/*.nanorc"' >> ~/.nanorc | |
| # close and re-open your terminal and you'll have syntax highlighting |
idan
/ gist:c27b2dd45a78273af848
Created
October 8, 2014 13:13
Exploding Postgres HSTORE columns in Pandas
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
| def explode_hstore(df, column): | |
| """Explode a column of a dataframe containing PostgreSQL hstore k-v pairs in the format of: | |
| "foo"=>"bar", "baz"=>"quux", ... | |
| Every key becomes a column. If a given row's pairs doesn't have a key, then the resulting column's value | |
| will contain NaN. | |
| """ | |
| # split the tags column out as a new series, and break up each k=>v pair | |
| s = df[column].str.split(', ').apply(pd.Series, 1).stack() |
pbugnion
/ ipython_notebook_in_git.md
Last active
October 22, 2023 12:25
Keeping IPython notebooks under Git version control
This gist lets you keep IPython notebooks in git repositories. It tells git to ignore prompt numbers and program outputs when checking that a file has changed.
To use the script, follow the instructions given in the script's docstring.
For further details, read this blogpost.
The procedure outlined here is inspired by this answer on Stack Overflow.
devhero
/ byobu_cheatsheet
Last active
July 21, 2024 00:56
byobu cheatsheet (from F9 -> quick start guide) - http://askubuntu.com/questions/661940/i-just-dont-get-byobus-keybindings-systems-or
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
| Byobu is a suite of enhancements to tmux, as a command line | |
| tool providing live system status, dynamic window management, | |
| and some convenient keybindings: | |
| F1 * Used by X11 * | |
| Shift-F1 Display this help | |
| F2 Create a new window | |
| Shift-F2 Create a horizontal split | |
| Ctrl-F2 Create a vertical split | |
| Ctrl-Shift-F2 Create a new session |
Clone this gist into the working directory
git clone git@github.com:96670d2eb66a8ad9854b6f52a2b5339c.git vagrant-ansible-neo
cd vagrant-ansible-neo
Install the neo4j role into the working directory
ansible-galaxy install julienroubieu.neo4j -p .
Bring up the vagrant box
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 | |
| ## Wrapper to interact with NCBI SRA using aspera ascp command line interface | |
| ## v 2.5 | 04/2017 | |
| ## @sbamin | |
| # More info: http://download.asperasoft.com/download/docs/ascp/2.7/html/ | |
| # usage | |
| show_help() { |
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
| { | |
| "mongod_log": { | |
| "title": "MongoDB server log format", | |
| "regex": { | |
| "main": { | |
| "pattern": "^(?<timestamp>\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}[,\\.]\\d+\\+\\d+)\\s+(?<level>\\w)\\s+(?<component>\\w+|-)\\s+\\[?(?<context>-?\\w+)?\\]\\s+(?<body>.*)$" | |
| } | |
| }, | |
| "level": { | |
| "critical": "F", |
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
| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
RyanSchu
/ How To: Sanger Imputation.md
Last active
January 16, 2020 13:17
Read the Sanger How-to page to make sure your vcf file meets all the requirements for Sanger imputation.
The preimputation steps for UMichigan and Sanger are relatively similar. The main difference is that VCF files are not split by chromosome under sanger imputation. I recommend carrying out the Michigan preimputation steps anyways. If you have already carried out the preimputation steps for U Mich imputation then the only other requirement will be to merge the chr.vcf files into one vcf file and sort the result.
#merge vcf files from list of files
bcftools concat --file-list ~/preimputation/vcf_list.txt -o merged.vcf
gzip merged.vcf
OlderNewer