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 python

"""
One-line description.


More elaborate description.
"""
import argparse

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

# -*- 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