####### | Intro to Piping |
#####E Heppenheimer, Summer 2018 

##If your coding habits are similar to mine, you probably generate a lot of intermediate file 
##I've known there was a way around this, but until recently I lacked the confidence to use it 
##Turns out its actually not so hard! 
##the basic gist is that one can use a "pipe" (|) in place of an output file to use the output of one command as input for the next

##########For example: 
##Keep only entries for which column 9=6 and then print column 5 

#in the old days, I would have done this in three steps: 
$ $9 == 2' inputfile > tempfile
$ awk '{print $5}' tempfile > outfile 
$ rm tempfile 

#I can condense this to a single line with the use of a pipe |

$ awk '$9 == 2' inputfile| awk '{print $5}' > outfile 

##But it doesn't have to stop there: 
##say I also wanted to sort the outfile: 

awk '$9 == 2' inputfile| awk '{print $5}'| sort > outfile 

####This is also useful for some basic commands to, like counting the number of files in a directory 

$ ls /directory/path| wc -l 

#### And many other examples that mitigate the need to write intermediate files 


#########One other thing to note about pipes is that they can be used within a grep commands to mean "or" 

##For example, this will retain any entry with the word Chromosome OR the word position. 
grep -E 'Chromosome|Position' infile > outfile 


##Now that you know, stop writing so many intermediate files!