grep

grep some_string file grep hypo multifastafile

1. includes some non hypothetical lines

grep hypothe multifastafile

1. increase the specificity of the string to match

grep –i some_string file

1. ignores case

grep trap multifastafile

1. only finds one line

grep -i trap multifastafile

grep some_string file |grep some_string

1. string together (pipe) several greps

grep -i trap multifastafile |grep TAXI grep -i trap multifastafile |grep TAXI |grep For

grep –v some_string file

1. 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

1. 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

1. won't work because of the special character

grep “>” tursiops.fa -c

1. 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