hi everyone,
I am trying to make a program in which I am making a subroutine and passing(returning) its values into a array and then printing it. Actually the values which are being passed are read by an scalar variable what I am not able to do is to store it in an array afterwards or maybe something else.
the program is as follows-
@a=data2();
print " the array is @a \n";
division(@a);
sub division(@a){
($tcount)=@a;
print "in division array is first $tcount \n";
}
sub data2(){
open (FH,"dataset2.txt");
%seq_dt2=<FH>;
@index2=keys%seq_dt2;
print "@index2";
$len2=@index2;
print "$len2";
$occ_f_6len_in_1000bp_seqfile=995;
$total_occurance= ($occ_f_6len_in_1000bp_seqfile * $len2)/6;
print "ref ka occurance h ye $total_occurance";
@seq2=values%seq_dt2;
chomp (@seq2);
print "@seq2";
open (FILE,"Motif6.txt");
@motif=<FILE>;
chomp @motif ;
print " @motif\n";
foreach $motif (@motif) {
foreach $seq2 (@seq2) {
if ($seq2 =~ /$motif/) {
$tcount++;
}
}
print "$motif $tcount \n";
print " $tcount \n";
return ("$tcount");
$tcount =0;
close (FH);
}
my dataset2 file is -
>1
ATGCATAAAAAAATCGACTAGCTACGATCGATCAGAAAAACACAC
>2
CAGCTAAAAAGCTACGAAAAAAATCGATAGCTAGAAAAACA
my motif6 file is-
AAAAAA
AAAAAT
AAAAAG
AAAAAC
the output which m getting is -
the array is 2
in division array is first 2
the desired output which i want is-
the array is 2,2,1,2
in division array is first 2,2,1,2
AAAAAA 2
AAAAAT 2
AAAAAG 1
AAAAAC 2
perl
programming
perl error
Your script is incorrect, it does not use strict or warnings! Non-strict scripts cannot be debugged efficiently. Also the example is lacking any real relation to bioinformatics, please point those out.
Please turn on strict and warnings, then the errors will become more obvious. Start your script like this:
sir, thankyou for pointing it......i will surely start doing it from now onwards. I just want this subroutine to return values in the @a which I called above, now what sort of bioinformatics connection you are trying yo ask is beyond my understanding. Its simply a programming mistake which m not able to debug how ever i will try using strict and warning right now.
The way your code is written, your subroutine is returning a scalar value,
return ("$tcount");not an array. If you want to return an array, store the values you want to return in an array variable.
I think the problem is that you are expecting the subroutine to return one value at a time, whereas once the program executes the return statement, control transfers to the main script, and will not continue executing the subroutine. What you need to do is store your results in an array inside the subroutine, then, at the end, return that array.
return ("@tcounts");Err, no!
but
Hello kriti.awasthi23!
We believe that this post does not fit the main topic of this site.
Not a bioinformatics question according to OP.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
Sir, I am working on some motif prediction projects in which I have to use programming and I am making a program to match motifs from the data set file and call them and build calculations for certain methods! This is pure bioinformatics work sir if it would not have been a bioinformatics query sir I wouldn't have posted it here! I am a beginner and I have to learn alot from your elder people guidance!
That is irrelevant, you have received at least one working solution (plus 2-3 alternative approaches and recommendations to use strict; use warnings; which you did not implement) to your last question perl programming query stating the identical problem, if you have further comments on the solution for the exact same problem there, please attend the first question. In your above comment you further state yourself that this is not a bioinformatics question, but pure programming. If I understand the core question correctly, then it is essentially "how do I return an array from a subroutine in perl?", which I do agree with you is basic perl programming. You will find many answers by searching the exact sentence I quote above.
Sir, Thankyou for your suggestions.I will keep all the important points in my mind.