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Hi rharsh, Thank you so much! Is "print "Pairs: ",@pairs,"\n";" to print the negative pairs? Thanks again!

the updated code as below: my @fullset = qw(AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT); my (@major, @minor, @combinations); { my @temp = @fullset; foreach (0..3) { my $r_pair = splice(@temp, int(rand($#temp+1)), 1); $major[$_] = $r_pair; } } foreach my $pos (0..$#major) {...

Hi,all! I am going to generate some nagative dependent nucleotide pairs and need your help. I have enclosed the description of the question and my code here. Any suggestion is highly appreciated. *********************************** The description To generate negative dependent pair...

It works! Thank fish!

hi fish, I doubt line 51 is within open OUTPUT, "> outfile9_55_$y.txt" or die "Cannot open output file.\n"; foreach (@combinations) { print OUTPUT join('', @{$_}), "\n"; } thanks

Hi rharsh! I tried that code. Although the message "Use of uninitialized value in join or string at make_file2.pl line 51" still exsited, it seemed that that code can generate the right results. Thank you again!

Thank rharsh for help! That code does work! But what is the problem in my first code? Thanks again! Alex

The intersting thing is that another very similar code runs well. I only changed the "fullset" in the above code but it turned out that the error message occured. The similar code is: #!/usr/bin/perl use strict; use warnings; my @fullset = qw(AA AC AG AT CA CC CG CT GA GC GG GT TA TC TG TT)...

Hi all, I got an error message when running the code at the end of this post. It said that "Use of uninitialized value in join or string at make_file2.pl line 51." Although I doubt the error message, I would appreciate if you can find something I really missed. Thank you! Alex...

Dear all, Thank you for warm help! I prefer "open (SHORT, "< outfile8.txt"); chomp (@short = <SHORT>); close SHORT;" for the input. BTW, can the code be slightly modified to print the result like: 37 26 26 56 32 22 36 47 (Note: each number is the highest frequency of the nucleotide in...

I see! Thank you! But can you remove the output like "0 | G 1 | A 2 | C 3 | T 4 | T 5 | G 6 | A 7 | A" ?

Hi Duncan, I put the data in the code and got the result like: 0 | C 1 | G 2 | A 3 | T 4 | T 5 | A 6 | G 7 | C 0 | T 1 | A 2 | C 3 | T 4 | T 5 | A 6 | G 7 | A 0 | A 1 | C 2 | C 3 | C 4 | A 5 | C 6 | C 7 | G 0 | C 1 | T 2 | G 3 | A 4 | G 5 | T 6 | T 7 | C 0 | T 1 | G 2 | T 3 | C 4 | A 5 | T...

should I include the data in the code?

Hi Duncan, I ran the 1st script. The output is: A: conclusion C: conclusion T: conclusion G: conclusion What is the problem? Thanks, Alex

Hi! I have a txt file which holds 100 sequences and the width for each sequence is 8 nucleotide long. Like: AGATAGCA ACACAGTA TCCGTGCT ATTGGCTA GACTTGAA ........ I want to calculate the frequency of nucleotides A,T,C,G for each column NOT each row and print them out. My code is here but it...

Hi rharsh, Thanks for the message! I changed the code as you suggested and run into the result like: CCAGCGCT CCAGCGCT AAATCGCT CCAGCGCT CCAGACCT AAAGCGCT CCAGACCT CCAGCGTG CCAGCGCT CCAGCGCT CCATCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCAGCGCT CCATCGCT CCAGCGCT CCAGACCT CCAGACCT...

Hi Kevin, Thanks! Since we had to change our ideas, the code should be changed slightly. BTW, I fixed another code which used subroutine. Thanks again!

Hi all, Thank you so much for help on this topic. After discussing with my advisor, we thought that we would have to switch to another idea because the previous data was not what we really want. My previous description was: ************************************************** I am going to...

Thanks! In case that I need the number other than 100, I guess I can change the probability accordingly. Right? Thanks!!!

so what is your suggestion? you mean it will generate more than 100 sequences?