bow

# -*- mode: ruby -*-
# vi: set ft=ruby :

# Vagrantfile API version
VAGRANTFILE_API = 2

# Set global VM name.
VM_NAME = ENV["VM_NAME"] || "stock"

# Environment-variable controlled config values with some defaults

bow

-- View index sizes and some of their stats, largest first.
SELECT idx.relname AS table_name,
       idx.indexrelname AS index_name,
       pg_size_pretty(pg_relation_size(cls.oid)) AS size,
       cls.reltuples AS num_tuples,
       idx.idx_scan AS num_scanned,
       idx.idx_tup_read AS num_read,
       idx.idx_tup_fetch AS num_fetched
  FROM pg_stat_user_indexes idx,
       pg_class cls,

bow

#!/usr/bin/env python

"""
One-line description.


More elaborate description.
"""
import argparse

bow

GTF (http://mblab.wustl.edu/GTF22.html)

• Coordinates are one-based, fully closed (i.e. position start at 1 and an interval's end position is included).
• (for files released by GENCODE & Ensembl) CDS include start_codon but not stop_codon. stop_codon is included in the UTR instead.

refFlat (https://genome.ucsc.edu/FAQ/FAQformat.html)

• Coordinates are zero-based, half open (i.e. position start at 0 and an interval's end position is not included).
• (for refFlat.txt.gz file available via UCSC) CDS does include start and stop codons

bow

#!/usr/bin/env sh

# Script for retrieving rRNA regions denoted in UCSC as a BED file.
# Requirements: mysql and an internet connection.

GENOME_BUILD=${GENOME_BUILD:-hg38}

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A --column-names=FALSE << QUERY
USE ${GENOME_BUILD};
SELECT genoName, genoStart, genoEnd, repName, swScore, strand

bow

for dep in `cat requirements.txt | grep -v git | sed 's/=.\+//g'`; do pip show $dep | grep Requires | sed 's/Requires: //g' | tr ", " "\n" | sed '/^$/d'; done | sort | uniq

bow

# -*- coding: utf-8 -*-

# Copyright (c) 2015 Wibowo Arindrarto <bow@bow.web.id>
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#

bow

name: vep-consequence-extract
dependencies:
- beautifulsoup4=4.4.1=py35_0
- libxml2=2.9.3=0
- libxslt=1.1.28=0
- lxml=3.6.0=py35_0
- openssl=1.0.2h=1
- pip=8.1.2=py35_0
- python=3.5.1=0
- readline=6.2=2

bow

#!/usr/bin/env sh
#
# sym2ensembl.sh
#
# Quick bash script for querying the Ensembl Gene ID given its gene symbol.
#
# Input : file containing gene symbols to query (one per line).
#
# Output: mapping between the gene symbol to its Ensembl Gene ID.
#

bow

Keybase proof

I hereby claim:

• I am bow on github.
• I am bow (https://keybase.io/bow) on keybase.
• I have a public key whose fingerprint is 07EF EC69 6E46 0E86 A036 8C94 D4EF 801C 7A10 C00C

To claim this, I am signing this object: