grep 

grep some_string file
grep hypo multifastafile
	-includes some non hypothetical lines
grep hypothe multifastafile
	-increase the specificity of the string to match

grep –i some_string file
	-ignores case
	grep trap multifastafile
		-only finds one line
	grep -i trap multifastafile
	
grep some_string file |grep some_string
	-string together (pipe) several greps 
grep -i trap multifastafile  |grep TAXI
grep -i trap multifastafile  |grep TAXI |grep For

grep –v some_string file
	-finds the lines WITHOUT the string
grep -i trap multifastafile  |grep TAXI |grep -v Rev

grep –i some_string  file--color
	grep -i trap multifastafile  |grep --color TAXI 
	grep -i trap multifastafile  |grep --color TAXI |grep -i forwa --color
		-color works on last match
	
	
grep -c some_string file
	-counts the number of lines
	grep 60S BS_named.gff3 --color
	grep 60S BS_named.gff3 -c gives 3568
	
grep -n some_string file
	grep 60S BS_named.gff3 -n
	grep -n 60S BS_named.gff3
	grep -n 60S BS_named.gff3 |more
	
grep ">" tursiops.fa
grep > tursiops.fa
	-won't work because of the special character
grep ">" tursiops.fa -c
	-fast way to find how many individual fasta files in a multifasta file
	
grep \> tursiops.fa -c
grep '>' tursiops.fa


 
can use regular expression but not covered here - just a taste
grep ^G tursiops.fa --color
	^ means must be at beginning of line
grep G$ tursiops.fa --color
	$ means must be at the end of the line
grep ^G[HMP] tursiops.fa --color
	[] hold character classes H or M or P in second postion
grep ^G[HMPL][G] tursiops.fa --color