bash script similar to javascript var.substring(start,end)

piman · 08-26-2011, 10:37 PM

I am looking for a way to verify the first the characters of an input and once verified continue taking input every three chars. My javascript code is: if (RNA.substring(0,3) != 'AUG') {

alert('You did not start with the first AUG codon!');

}

if (RNA.substring(0,3) == 'AUG') {

result.push('M/Start');

}

for (i=0;i<=100;i++) {

if (RNA.substring(start,stop) == '"B"') {

result.push('B');

var start = start+3;

var stop = stop+3;

}
so I need a similar way to do this in bash. I know how to do a for loop but I do not know how to take input in three characters at a time.
Any help is appreciated as I am pretty new to Bash.
Thanks in advance!

thesnow · 08-29-2011, 12:15 PM

Using this page as a guide http://www.cyberciti.biz/faq/linux-u...me-while-loop/ you can probably make something work, if you have your input string in a file on the file system.

Code:

[user@vm:~/testing]$ cat INPUT
ABCDEFGHIJKLMNOPQRSTUVWXYZ


[user@vm:~/testing]$ cat arraytest.bash 
#!/bin/bash

while IFS= read -r -n3 char
do
echo $char
done < "./INPUT"


[user@vm:~/testing]$ ./arraytest.bash 
ABC
DEF
GHI
JKL
MNO
PQR
STU
VWX
YZ

kurumi · 08-29-2011, 07:54 PM

With bash, you can do index slicing as well, eg

Code:

${string:0:3}

piman · 09-02-2011, 09:17 PM

Thank you both for your answers. kurumi's answer looks easier, but I had already rewritten the script with thesnow's answer and I do not want to redo it again. If anyone cares the full script will be posting shortly at http://mikedombrowski.com/mrna.bash