John McCallum cfljam

30 followers · 5 following

Plant and Food Research
New Zealand
http://cfljam.github.io/

View GitHub Profile

Recently created

Least recently created

Recently updated

Least recently updated

cfljam / gist:8948348

Last active August 29, 2015 13:56

Minimalist Approach to Documentation

[cfljam@genome3 ~]$ cd /workspace2/genome_analysis/plant/Actinidia/chinensis/20Monkeys/
[cfljam@genome3 20Monkeys]$ pwd
/workspace2/genome_analysis/plant/Actinidia/chinensis/20Monkeys
[cfljam@genome3 20Monkeys]$ ls
Fastqc  Haplotyping  mappedtoHY  README.md  Reads  RedOrDead  SexSexSex  temp_opt
[cfljam@genome3 20Monkeys]$ cat > README.md

Analysis of Actinidia Whole Genome Sequencing 2013

cfljam / gist:9943916

Created April 2, 2014 21:49

Delete Un-named columns from a Pandas Dataframe read from Excel

DF.drop([Y for Y in DF.columns if re.compile('Unnamed*').match(Y)],1)

cfljam / new_gist_file.sh

Created May 16, 2014 21:59

Create a bed genome file from a compressed fast reference

zcat my_reference.fa.gz | awk -v OFS="\t" '/^>/{print substr($1,2),$2}' > my.genome

cfljam / In Silico PCR with IPCRESS.ipynb

Created June 2, 2014 08:36

Using IPCRESS for electronic PCR, and parsing output

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

cfljam / HRM Design from BSA RNASEQ Variants.ipynb

Created June 19, 2014 01:21

Design of HRM Assays for Validation of SNPs revealed by Poolseq

Sorry, something went wrong. Reload?

Sorry, we cannot display this file.

Sorry, this file is invalid so it cannot be displayed.

cfljam / .screenrc

Created July 9, 2014 07:03

.screenrc for Unix screen

	hardstatus alwayslastline
	hardstatus string '%{= kG}[ %{G}%H %{g}][%= %{=kw}%?%-Lw%?%{r}(%{W}%n*%f%t%?(%u)%?%{r})%{w}%?%+Lw%?%?%=%{g}][%{B}%Y-%m-%d %{W}%c %{g}]'
	defscrollback 4242

cfljam / gist:1f4a8cfcb522eab3433d

Last active August 29, 2015 14:05

Shell Installation of Scientific Python for Vagrant

	#!/bin/sh
	sudo apt-get -y update
	sudo apt-get -y install curl build-essential python-dev python-pip python-numpy python-scipy git
	sudo pip install --upgrade distribute
	sudo pip install --upgrade ipython[all]
	sudo pip install --upgrade pyzmq jinja2 numpy tornado pandas scipy

	## Primer design pre-requisites
	sudo pip install Biopython
	sudo pip install bcbio-gff

cfljam / Vagrantfile

Last active August 29, 2015 14:05

Using Vagrant Behind a Firewall

	#### Place this in $HOME/.vagrant.d/ or append to the Vagrantfile there
	## eidting the proxy user,pwd, address and port accordingly

	Vagrant.configure('2') do \|config\|
	if Vagrant.has_plugin?("vagrant-proxyconf")
	config.proxy.http = "http://proxy.my_org.com:8080"
	config.proxy.https = "https://proxy.my_org.com:8080"
	config.proxy.no_proxy = "localhost,127.0.0.1,.example.com"
	end
	end

cfljam / new_gist_file.r

Created September 2, 2014 06:43

change terminal letter code in Kiwi item to lowercase

gsub("(.+)([A-Z])$","\\1\\L\\2",my_df$Pedigree_item, perl=TRUE)

cfljam / split_fasta

Created September 21, 2014 23:52

Split multi-fasta file into individual files

awk '/^>/{s=++d".fasta"} {print > s}'

Older Newer