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Computational Techniques for Life Sciences

STRINGS

We’ve seen earlier that bash STRINGS are groups of characters.

Can we manipulate these strings inside bash scripts?

Parameter substitution for strings

Earlier we learned that surrounding a variable with ${} indicates you want to treat it as a parameter and access more information about the variable.

Here are some additional parameter substitutions to help you strings:

${#string} : length of string.

prompt> a="apple"
prompt> echo ${#a} ${a}
5 apple

${string:position:length} : substring starting at position for length characters.

prompt> file=1j6z.pdb
prompt> echo ${file:0:4}
1j6z
prompt> echo ${file:(-3):2}
pd

expr index string substring : returns position at which substring starts

prompt> file=1j6z.pdb
prompt> ix=$(expr index $file ".pdb")
prompt> echo ${file:$((--ix))}
.pdb
prompt> echo ${file:0:$ix}
16jz

${string/substring/replacement} : substitute substring for replacement for / = first or // = all occurrences of substring.

prompt> file=fp_math.sh
prompt> echo ${file/h/#}
fp_mat#.sh
prompt> echo ${file//h/#}
fp_mat#.s#
prompt> echo ${file//h/}
fp_mat.s

Expression	Meaning
${#string}	Length of $string
${string:position}	Extract substring from $string at $position
${string:position:length}	Extract $length characters substring from $string at $position
${string#substring}	Strip shortest match of $substring from front of $string
${string##substring}	Strip longest match of $substring from front of $string
${string%substring}	Strip shortest match of $substring from back of $string
${string%%substring}	Strip longest match of $substring from back of $string
${string/substring/replacement}	Replace first match of $substring with $replacement
${string//substring/replacement}	Replace all matches of $substring with $replacement
${string/#substring/replacement}	If $substring matches front end of $string, substitute $replacement for $substring
${string/%substring/replacement}	If $substring matches back end of $string, substitute $replacement for $substring

expr match “$string” ‘$substring’	Length of matching $substring* at beginning of $string
expr index “$string” $substring	Numerical position in $string of first character in $substring that matches

EXERCISE: given a filename and an extension create a script that adds “_old” before the extension.

prompt> vi cp_old.sh

#!/bin/bash

file=$1
ext=$2

ix=$(expr index $file $2)
base=${file:0:$((--ix))}
cp ${file} "${base}_old${ext}"

prompt> touch 1j6z.pdb
prompt> ls 1j6z*
0 1j6z.pdb
prompt> ./cp_old.sh 1j6z.pdb .pdb
prompt> ls 1j6z*
0 1j6z_old.pdb  0 1j6z.pdb