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