#Basic use of grep for regular expressions 
#E Heppenheimer, Fall 2017 


#basic syntax is: 
$ grep searchterm infile > outfile

#For a more specific example: 
$ grep exon infile > outfile
#will print every line that contains the word "exon" in the infile to the outfile 
#if you don't include "> outfile", this information will print to the terminal window 


#if you are searching for more than one word with grep, you need and -E flag and '' around the phrase you are looking for 

$ grep -E 'number of reads' infile > outfile

#if you want to looks for lines that contain one of multiple possible phrases, you can use a pipe (|) to signify "or" 
#this will print every line that contains at least one of these phrases 

$ grep -E 'Identifying unique reads|Number of utilized reads' infile > outfile