jaymecd

Pivot JSON data

This one-liner pivots data from group>users or user>groups:

$ cat incoming.json \
  | jq 'map(. as $in | .users[] | . as $u | {user:$u, group:$in.group}) | group_by(.user) | map({user:.[0].user, groups: map(.group)})'

[
 {

hurrialice

import igv_remote as ir
import keyboard
import numpy as np
import pandas as pd

cohort = "BRCA"
print("cohort: {}".format(cohort))
# generate localhost http format
def format(uuid):
    return("http://localhost:5000/" + uuid + ".bam")

hurrialice

#' better display and logging backend
#' 
#' @param expr expression to evalutate
#' @param tag_width The width of display box of the message tag 
#' @param path where the message goes, default to `stdout()`
#' @param save_conditions if `TRUE`, all conditions will be saved to a list
#' @param quiet if `TRUE`, all messages (error excluded) will be suppressed
#' @examples 
#' test_function <- function(){

elowy01

*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

mohanpedala

Table of Contents

• set -e, -u, -x, -o pipefail
• set -e
• set -x
• set -u
• set -o pipefail
• Setting IFS
• Original Reference

set -e, -u, -x, -o pipefail

aklap

Resolving missing link to libcrypto openssl on OSX from: http://stackoverflow.com/questions/38670295/brew-refusing-to-link-openssl

brew update

brew install openssl

ln -s /usr/local/opt/openssl/lib/libcrypto.1.0.0.dylib /usr/local/lib/

ln -s /usr/local/opt/openssl/lib/libssl.1.0.0.dylib /usr/local/lib/

olih

Processing JSON using jq

jq is useful to slice, filter, map and transform structured json data.

Installing jq

On Mac OS

brew install jq

joar

# Add field
echo '{"hello": "world"}' | jq --arg foo bar '. + {foo: $foo}'
# {
#   "hello": "world",
#   "foo": "bar"
# }

# Override field value
echo '{"hello": "world"}' | jq --arg foo bar '. + {hello: $foo}'
{

ajaegers

Change structure of project folder with Git

I have this structure:

 project-folder/
     .git
     wp-admin/
     wp-content/
     wp-includes/

.htaccess

benmarwick

---
title: "Auto-numbering and cross-referencing of figures and tables in rmarkdown"
output: html_document
---

NOTE: I recommend using the bookdown package and `output: html_document2` to make captions and cross-references more easily than the method described below. 

TODO: check this out: https://github.com/adletaw/captioner

Here's how to use: