bash script that receives any sequence of nucleotides and print all positions of the T nucleotides

Question

I need to write a bash script that receives any sequence of nucleotides and print all positions of the T nucleotides.

I did the following:

'vim nucleotide.sh' inside the script

#!/bin/bash
$@
cat $@ | while read line;do echo $line | grep -i t;done

But when I ran the script on new.dat sequence file

$ bash nucleotide.sh new.dat

it displays all sequences without marking T position, however when I run cat $@ | while read line;do echo $line | grep -i t;done outside the script, it displays the sequences with T colored in red. Any suggestions, please

I'm not sure what the second line in your script is supposed to do — knittl, Apr 15 '23 at 19:57
Please add sample input (no descriptions, no images, no links) and your desired output for that sample input to your question (no comment). — Cyrus, Apr 15 '23 at 19:59

score 1 · Answer 1 · answered Apr 15 '23 at 20:34

If you want to search for the 't' in the input, you can feed it directly to 'grep', no need to use bash while read ... ; echo ..., or even the cat. You can use grep -h or --no-filename to eliminate file name (in case multiple file names are provided)

grep --color=always -i t -- "$@"
# OR
cat "$@" | grep --color-always -i -t
# OR
grep --color-always -h -i t -- "$@"

bash script that receives any sequence of nucleotides and print all positions of the T nucleotides

1 Answers1