mkweskin’s gists

mkweskin / gist:2b1a1daad1cc68707e77fe3f6a2729c5

Created September 7, 2018 18:58

Ping an ip every 5 seconds and log output. ping options work on Mac, not sure about other OS's

while [ 1 ]; do date; ping -o -q -t 3 x.x.x.x >/dev/null && echo PASS || echo FAIL; sleep 5; done >~/pinglog

mkweskin / conda-orffinder.sh

Created September 6, 2017 14:33

Use conda's libgcc for NCBI's ORFfinder

	#Create new env with conda libgcc
	conda create -n ORFfinder -c anaconda libgcc
	source activate ORFfinder

	#Setup scripts to set LD_LIBRARY_PATH
	mkdir -p $CONDA_PREFIX/etc/conda/activate.d
	mkdir -p $CONDA_PREFIX/etc/conda/deactivate.d

	cat <<EOF >$CONDA_PREFIX/etc/conda/activate.d/LD_PATH.sh
	export LD_LIBRARY_PATH_CONDA_BACKUP=$LD_LIBRARY_PATH

mkweskin / rmssh

Created May 2, 2017 13:21

Removes a line from ~/.ssh/known_hosts. Takes a number as an argument or prompts for number. (written for sed version of macOS, YMMV)

	#!/bin/bash

	if [ -n "$1" ] #If input arg is non-empty then move on, but if it is prompt for number
	then
	LINE="$1"
	else
	echo "Enter line to delete of ~/.ssh/known_hosts:"
	read LINE
	fi

mkweskin / avgQseq

Created April 6, 2017 19:00

Gives the average Q value for each sequence in a fastq

	#!/usr/bin/env python
	import numpy as np
	from Bio import SeqIO

	for record in SeqIO.parse("test_R1.fq", "fastq"):
	print ('{}\t{}'.format(record.id, np.mean(record.letter_annotations["phred_quality"])))

mkweskin / avgQseq

Created April 6, 2017 19:00

Gives the average Q value for each sequence in a fastq

	#!/usr/bin/env python
	import numpy as np
	from Bio import SeqIO

	for record in SeqIO.parse("test_R1.fq", "fastq"):
	print ('{}\t{}'.format(record.id, np.mean(record.letter_annotations["phred_quality"])))

mkweskin / gist:9214338

Created February 25, 2014 18:03

Git clone with no cert check

env GIT_SSL_NO_VERIFY=true git clone https://...

mkweskin / keep-longest.py

Last active March 15, 2019 14:10

Keep longest sequence when there are duplicate descriptions in FASTA file: Reads a FASTA file and if >1 sequence has the same description line, it only keeps the longest sequence. It outputs all the sequencs to stdout when complete.

	#!/usr/bin/python

	"""
	Reads a FASTA file and if >1 sequence has the same description line,
	it only keeps the longest sequence. It outputs all the sequencs to stdout
	when complete.

	"""

mkweskin / gist:5831102

Created June 21, 2013 13:25

Mount the volume named "Time Machine" from the terminal (Mac)

diskutil mount `diskutil list | grep "Time Machine" | awk {'print $7'}`

mkweskin / gist:5542669

Created May 8, 2013 18:50

MacOS utility to enable/disable root access (don't call with sudo, the program authenticates for you)

dsenableroot

mkweskin / gist:5495586

Last active December 16, 2015 20:49

Basic symbolic link: first is source, second is link name

ln -s SATe-2.2.7 SATe

Matthew Kweskin mkweskin