UNIX

UNIX is the second largest computer operating system (next to Microsoftís OSís). It is used by MacOS and several versions of Linux but is also distributed freely (e.g. Ubuntu, openSUSE) , for use by those with PCs. There are many different flavors of UNIX, but the basics are shared between them all. Most researchers needing to do computer intensive tasks and/or programming use UNIX because it is more stable and faster than Microsoft OSís and it has many tools (e.g., grep, awk, sed) useful for such tasks.

I include a page on UNIX here because many things that can be done in R can be done using UNIX more quickly. This page just has a few snippets of code for my own use and for members of my lab. These commands can often be done from within R using the system() command, which I demonstrate after each UNIX command

 

#To take the 1st, 3rd, and 7th column and put it into a new file
awk '{print $1,$3,$7}' ~/Downloads/genotypes_chr5_CEU_r27_nr.b36_fwd.txt > pos.chr5
R> system(paste("awk '{print $1,$3,$7}' ~/Downloads/genotypes_chr",i,"_CEU_r27_nr.b36_fwd.txt > pos.chr",i,sep=''))

 

#get a list of every element of the 2nd column where the 5th column is greater than .1
awk '{if($5 < .1) print $2;}' maf.chr.5.frq > maf.5
R> paste("awk '{if($5 < .1) print $2;}' maf.chr.",i,".frq > maf.",i,sep="")

 

#to write a bash script that loops through chromosomes
#!/bin/bash
for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
do
   cbatch "plink --bfile /home/GWAS/GeneralRelease/Imputed/Release3/CleanPlink/GRclean${i} --extract  c${i}.keep1 --maf .05 --out GRclean2 --make-bed"
done

 

grep -A 1 'New Chomosome AFTER' log_POPNA_20Mb_neutral.out > ss.out #get lines after "new Cho.."
tail -n 600 ss.out > ss2.out #get last 600 lines
grep -v 'New Chomosome AFTER' ss2.out > ss3.out #get all lines BUT "New Chomo..."
grep -ve '--' ss3.out > ss4.out # e is necessary because "-" has special meaning in grep
grep -A 40 'Loop 99' log_POPNA_20Mb_neutral.out > s99.out #to check that new.hap lines up with pedigree file

 

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