bow

#!/usr/bin/env python

"""
Script for changing all absolute links in a given directory to symlinks, UNIX only.


Requirements:
    * Python >= 2.7.x or Python 3.x

Author:

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:

bow

#!/usr/bin/env python

import random

from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC

# function to generate random protein sequence

bow

#!/usr/bin/env python

# quick script to compare SearchIO and NCBIXML blast xml parser performance


searchio="""
from Bio import SearchIO

for result in SearchIO.parse('%s', 'blast-xml'):
    query_id = result.id

bow

Command line: [exonerate -m cdna2genome ../scer_cad1.fa /media/Waterloo/Downloads/genomes/scer_s288c/scer_s288c.fa --bestn 3]
Hostname: [blackbriar]

C4 Alignment:
------------
         Query: gi|296143771|ref|NM_001180731.1| Saccharomyces cerevisiae S288c Cad1p (CAD1) mRNA, complete cds
        Target: gi|330443520|ref|NC_001136.10| Saccharomyces cerevisiae S288c chromosome IV, complete sequence:[revcomp]
         Model: cdna2genome
     Raw score: 6146
   Query range: 0 -> 1230

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

-- 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

# -*- 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

#!/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