%%bash
date
Mon May 2 15:09:35 PDT 2016
%%bash
system_profiler SPSoftwareDataType
Software: System Software Overview: System Version: OS X 10.9.5 (13F34) Kernel Version: Darwin 13.4.0 Boot Volume: Hummingbird Boot Mode: Normal Computer Name: hummingbird User Name: Sam (Sam) Secure Virtual Memory: Enabled Time since boot: 14 days 5:14
%%bash
#Uses grep to exclude lines that display serial number and hardware UUID
system_profiler SPHardwareDataType | grep -v [SH][ea]
Model Name: Xserve Model Identifier: Xserve3,1 Processor Name: Quad-Core Intel Xeon Processor Speed: 2.26 GHz Number of Processors: 2 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache (per Processor): 8 MB Memory: 24 GB Processor Interconnect Speed: 5.86 GT/s Boot ROM Version: XS31.0081.B06 SMC Version (system): 1.43f4 LOM Revision: 1.1.8
cd /Volumes/toaster/sam/scratch/
/Volumes/toaster/sam/scratch
ls
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq 20160428_Oly_GBS_stacks/
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq
%%bash
head -4 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq
@K00132:90:H3YHMBBXX:4:1101:1316:1173 1:N:0:NAGGATGC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC + AAAFFJJFJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJAJFJJJJJJJJJ
%%bash
head -5 OlyGBS_BarcodeMap.txt
NCTCC CTCC NTGCA TGCA NACTA ACTA NCAGA CAGA NAACT AACT
%%bash
time while read line; do neww=${line##* }; oldw=${line%% *}; sed -i '/@/s/$oldw/$neww/g' 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq; done < OlyGBS_BarcodeMap.txt
sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ sed: 1: "160123_I132_FCH3YHMBBXX ...": invalid command code _ real 0m0.234s user 0m0.098s sys 0m0.135s