In [1]:

!date

Wed Apr 27 16:12:57 PDT 2016

In [2]:

%%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: 9 days 6:19

In [3]:

%%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

Add to md5 checksums file¶

In [1]:

%%bash

#For loop generates a md5 checksum has value for each file
#and appends the output to the checksums.md5 file.
time for file in /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_[12].fq.gz
    do
        md5 "$file" >> /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5
        done

real	12m58.000s
user	1m44.985s
sys	0m28.281s

Calculate total number of reads generated by this project.¶

Calculate number of reads per file, append filename and corresponding number of reads to readme file.¶

In [3]:

%%bash

#Initializes variable.
totalreads=0

#For loop counts the lines in each file and divides them by four. This is performed because
#Illumina sequencing files are composed of four lines per read.
#A running total of the total number of reads is generated [totalreads=$((readcount+totalreads))]
#and is printed after the for loop completes.

#Format the output (printf) to print the filename, followed by a tab, followed by the readcount.
#The command "tee -a" is used to both print the output to the screen and append the output to the readme.md file.
time for file in /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_[12].fq.gz
    do linecount=`gunzip -c "$file" | wc -l`
    readcount=$((linecount/4))
    totalreads=$((readcount+totalreads))
    printf "%s\t%s\n\n" "${file##*/}" "$readcount" | tee -a /Volumes/owl_web/nightingales/O_lurida/20160223_gbs/readme.md
done
echo $totalreads

160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz	364261046

160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz	364261046

728522092

real	29m40.999s
user	18m34.488s
sys	1m58.738s