mjhjmtu

The assignment is to write a bash script named countmatches that will display the number of times a certain sequence, such as aac appears in a specific file. The script should expect at least two commands in which the first argument has to be the pathname of a file containing a valid DNA string which we are given. The remaining arguments are strings containing only the bases a, c, g, and t in any order. For each valid argument string, it will search the DNA string in the file and count how many non-overlapping occurrences of that argument string are in the DNA string.

An example sequence and output would be if the string aaccgtttgtaaccggaac is in a file named dnafile, then your script should work as follows

$ countmatches dnafile ttt

ttt 1

with the input being "count matches dnafile ttt" and the output being "ttt 1" showing that "ttt" appears once.

this is my script:

 #!/bin/bash

 for /data/biocs/b/student.accounts/cs132/data/dna_textfiles

 do

 count=$grep -o '[acgt][acgt][acgt] /data/biocs/b/student.accounts/cs132/
 dna_textfiles | wc -w

 echo $/data/biocs/b/student.accounts/cs132/data/dna_textfiles $count

 done

and this is the error I get

 [Osama.Chaudry07@cslab5 assignment3]$ ./ countmatches /data/biocs/b/student.accounts/cs132/
 data/dna_textfiles aac

 ./countmatches: line 6: '/data/biocs/b/student.accounts/cs32/data/dna_textfiles': not a valid identifier

cat dna_textfile 
aaccgtttgtaaccggaac 

#!/bin/bash 
dna_file=/autofs/cluster/atassigp/garbage/dna_textfiles
printf "e[31mnucleotide sequence?:";
read -en 3 userInput
while [[ -z "$userInput" ]]
do
read -en 3 userInput
done

count=$(grep -o "$userInput" $dna_file | wc -l)

echo "$userInput", $count

output:

 ttt, 1