Some issues in HW1

• Reproducibility: absolute path or relative path?

  nsnps=$(wc -l < /home/m280-data/hw1/merge-geno.bim)
  echo "    2.40 = FILE FORMAT VERSION NUMBER." > mendel_snpdef.txt
  echo " $nsnps = NUMBER OF SNPS LISTED HERE." >> mendel_snpdef.txt
  time awk '
  {OFS = ","} 
  {print $2, $1, $4}
  ' /home/m280-data/hw1/merge-geno.bim >> mendel_snpdef.txt
  

  or

  nsnps=$(wc -l < /home/m280-data/hw1/merge-geno.bim)
  echo "    2.40 = FILE FORMAT VERSION NUMBER." > /home/huazhou/biostatm280-2018winter/hw1/mendel_snpdef.txt
  echo " $nsnps = NUMBER OF SNPS LISTED HERE." >> /home/huazhou/biostatm280-2018winter/hw1/mendel_snpdef.txt
  time awk '
  {OFS = ","} 
  {print $2, $1, $4}
  ' /home/m280-data/hw1/merge-geno.bim >> /home/huazhou/biostatm280-2018winter/hw1/mendel_snpdef.txt
  

Today

• String manipulations using stringr (cont’d).

• Shiny.