UNIX for Dummies Questions & Answers

I have a DNA file like below and I am able to write a short program which finds/not an input motif, but I dont understand how I can include in the code to report which position the motif was found. Example I want to find the first or all "GAT" motifs and want the program to report which position (beginning to end) of the dna motif was found. So in this example GAT (in bold should report 10-12) and if found more than once the other positions too. Can someone explain how to report matching position on strings ??

Thank you very much

Code:

>MY_DNA  
CAGCAGCAAGATTTGCAGCAACAGCAACAAGTAGTGACTACAGTTGCCTCGCAAAGTCCT
CATGCAACTGCAACGGAAAAGGAGCCAGTACCCGCCGTGGTTGACGACCCACTGGAGAAC
ATGTTCGGAGATTATTCCAATGAGCCGTTCAACACCAATTTCGACGATGAATTTGGAGAT

What is your system? What is your shell?

---------- Post updated at 09:24 AM ---------- Previous update was at 09:18 AM ----------

dna.awk:

Code:

{
        LINE++;
        for(N=0; N<(length($0)-length(STR)); N++)
        if(STR == substr($0, N, length(STR)))
                printf("Line %d, position %d\n", LINE, N);
}

Code:

$ awk -f dna.awk -v STR="GAT" dnafile
Line 1, position 10
Line 3, position 10
Line 3, position 46
$

---------- Post updated at 09:35 AM ---------- Previous update was at 09:24 AM ----------

Slight modification to dna.awk:

Code:

{
        LINE++;
        for(N=0; N<(length($0)-length(STR)); N++)
        if(STR == substr($0, N, length(STR)))
                printf("Line %d, %d-%d\n", LINE, N, N+length(STR));
}

I use bash shell

Is there a Perl way to do that coz I'm trying to learn Perl and want to know how to do this with Perl.

Thanks

If you want to treat that those lines as one string:

Code:

perl -ln0e '$x="GAT";s/>.*//;s/\n//g;while(/(.*?)$x/g){print ((length $1) + 1 + $sum . "-" . ((length $&) + $sum));$sum+=length $&}' file

@Bartus11
Here comes again another one of your amazing one-liners ... could you please comment on the code Here are the parts which I think I understand: Correct me if I'm wrong please

The rest of it I didnt understand, please could you explain?

Thank you very much

-l "chomps" $_ variable, meaning it removes only last newline. To remove newlines that are inside of the input string, s// has to be used.

Code:

while(/(.*?)$x/g){

This is a bit tricky piece. It is matching sequentially on $_ variable, and when match is found, the body of while loop is executed. So for each match in a string, the code of while's body will be executed.
print ((length $1) + 1 + $sumIt will print starting position of the searched pattern. It is achieved by getting the number of characters before that string - length $1 ($1 stores match of the red part in regular expresion). To make it possible to print subsequent positions (after first match), the number of characters from the beginning of the string has to be saved. It is done by $sum.
((length $&) + $sum)This will calculate ending position of pattern to search ($& is a variable containing whole string matched by the regex, so length $& will get number of characters before searched pattern + length of that pattern.
$sum+=length $&As I wrote before, $sum is saving the number of characters that regex already passed through.

That made it more understandable .... thanks