knmkr

A simple example to link tabix C library into GO language.

1. download tabix C source code
2. make dynamic libtabix.so.1 [ or make to get libtabix.a]
3. cp libtabix.so.1 to your LD_LIBRARY_PATH [ or use the static version libtabix.a ]
4. mv query_tabix_example.go query_tabix.go query_tabix_example_static.go into tabix directory which contains example.gtf.gz and example.gtf.gz.tbi and libtabix.a
5. go run query_tabix_example.go [ or go run query_tabix_example_static.go ]
6. go run query_tabix.go [file.bed] [file.gz]
7. query_tabix_bed6.go are designed for query motifs and coordinates translate to query region.

knmkr

Tabix command of htslib can query a locus to a remote s3 file using s3:// protocol.

$ aws s3 ls s3://your_bucket/
vcf.gz
vcf.gz.tbi

$ tabix -l s3://your_bucket/vcf.gz
chr1
chr2

knmkr

from requests_oauthlib import OAuth2Session
from flask import Flask, request, redirect, session, url_for
from flask.json import jsonify
import os

app = Flask(__name__)


# This information is obtained upon registration of a new GitHub
client_id = "<your client key>"

knmkr

/reports

Endpoints

GET /v1-dev/reports/<phenotype_name>?population=<population>

param types	key	required	description
path param	phenotype_name	TRUE
query param	population	TRUE	currently only european is a valid value. other population is not available now.

knmkr

/genomes

Endpoints

GET /v1-dev/genomes/sequence/?<params>

Query params

params	style	description

knmkr

var https = require('https');
var util = require('util');

exports.handler = function(event, context) {
    console.log(JSON.stringify(event, null, 2));
    console.log('From SNS:', event.Records[0].Sns.Message);

    var postData = {
        "text": "*" + event.Records[0].Sns.Subject + "*",
    };

knmkr

# NCBI36
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/BUILD.36.3/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg18.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg18 /tmp/hg18.seq_gene.sorted.md 'reference'
mutalyzer-admin assemblies import-reference -a hg18 'NC_001807.4'

# GRCh37
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/ANNOTATION_RELEASE.105/initial_release/seq_gene.md.gz -O - \
  | zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg19.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg19 /tmp/hg19.seq_gene.sorted.md 'GRCh37.p13-Primary Assembly'

knmkr

I needed a way to have my Django ElasticBeanstalk application automatically redirect HTTP requrests to HTTPS. Rick Christianson wrote a post [1] about how to do this by overwriting the wsgi.conf file with one that was slightly modified to support the HTTP to HTTPS redirect.

Building off the shoulders of giants, I wanted to do the same, but not have to keep a copy of the config file in my local source directory. Christianson even points out in his post that if ElasticBeanstalk ever changes it's template for the wsgi.conf file, those updates would not be overwritten and you wouldn't get their benefits. To get around that problem, I used sed to insert the new lines into the wsgi.conf file.

References

1. http://rickchristianson.wordpress.com/2013/11/02/updating-wsgi-automatically-in-amazon-aws/
2. http://docs.aws.amazon.com/elasticbeanstalk/latest/dg/customize-containers-ec2.html#customize-containers-format-container_commands

knmkr

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import argparse
import smtplib

FROM = 'myserveradmin@gmail.com'

def _main():
    parser = argparse.ArgumentParser(description='')

knmkr

#!/usr/bin/env bash

# https://raw.githubusercontent.com/andsens/homeshick/master/lib/log.sh
# https://raw.githubusercontent.com/andsens/homeshick/master/lib/exit_status.sh
source "lib/exit_status.sh"
source "lib/log.sh"

info 'foo' 'bar'
warn 'foo' 'bar'