wakimchris

wakimchris / gist:3866fe1af97b0a1ec219

Last active August 29, 2015 14:16 — forked from taoliu/gist:5861468

perl -ne 'if (/^(\S+\/1)\:([ATCGN]+)\:(\S+)$/){print "@",$1,"\n",$2,"\n","+\n",$3,"\n";}' a.txt > a.fastq

wakimchris / txtToFastq.pl

Last active August 29, 2015 14:16 — forked from sashaphanes/txtToFastq.pl

	#!/usr/bin/perl -sw

	# sample inputs:
	#ILLUMINA-A93428 66 1 1 7848 1267 CGATGT 1 ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB chrX.fa 122287709 R 40C21GAC7 269 Y

	# output for sample input:
	#@ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
	#ATGTTGGCTGGCGGTGAAATAAATCTCAAACGTACCTGTTACAAAATTGTGTTAATCCTTTCAGATTCGCAG
	#+ILLUMINA-A93428:66:1:1:7848:1267:#CGATGT/1
	#ggggggggggggggcfdffdgggfefffffcfcffcccacBeddddded_cffefgggggBBBBBBBBBBBB

wakimchris / numpy_os_x_10_9.sh

Last active August 29, 2015 14:08 — forked from goldsmith/numpy_os_x_10_9.sh

	# set up flags for Numpy C extentions compiling
	export CFLAGS="-arch i386 -arch x86_64"
	export FFLAGS="-m32 -m64"
	export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch i386 -arch x86_64"
	export CC=gcc-4.2
	export CXX="g++ -arch i386 -arch x86_64"

	pip install numpy
	# success!