how to integrate (link togetger) these codes? 2

[Everwood]

Hi all!

I have two separate codes and want to integrate
them into one.

(1)1st code is to use a short sequence of width as 8 or 16
as a template to generate 100 short sequences of the same
width and store them in a txt file A.

(2)2nd code is to read 100 short sequences from the txt file A and 100 long sequences of width 200 from a txt file B and then replaced a substring of each long sequence using each short sequence. This code will lead to two txt files C and D. File C will hold 100 replaced long sequences while D will hold the starting sites of each replacement.

Since I need to generate 200 file C or more, that will be tedious for me to input the short template sequence each time mannually.

I hope to integrate these two codes as one to handle a file E which holds 200 short template sequences. And the output should be 200 file C.

Can anybody suggest me how to do this? I am appending my two codes here.

Thank buddies,



1st code
*******************************************************
#!/usr/bin/perl
use strict;
use warnings;
my $N_Sequences = 100;
my @Motif = split(//,'TTTATAAT'); # This is the template short sequence

my @Alphabet = split(//,'ACGT');
my $P_Consensus = 0.85; # This is the probability of dominant letter
# ====== Globals ==========================
my @Probabilities; # Stores the probability of each character
# ====== Program ==========================

open (OUT_NORM, ">short_sequences16_1.txt") or die "Unable to open file :$!";
for (my $i=0; $i < $N_Sequences; $i++) {
for (my $j=0; $j < scalar(@Motif); $j++) {

loadConsensusCharacter($Motif[$j]);
addNoiseToDistribution();
convertToIntervals();
print OUT_NORM (getRandomCharacter(rand(1.0)));
}
print OUT_NORM "\n";
}

exit();

# ====== Subroutines =======================
#
sub loadConsensusCharacter {
my ($char) = @_;
my $Found = 'FALSE';

for (my $i=0; $i < scalar(@Alphabet); $i++) {
if ( $char eq $Alphabet[$i]) {
$Probabilities[$i] = 1.0;
$Found = 'TRUE';
} else {
$Probabilities[$i] = 0.0;
}
}
if ($Found eq 'FALSE') {
die("Panic: Motif-Character\"$char\" was not found in Alphabet.
Aborting.\n");
}

return();
}

# ==========================================
sub addNoiseToDistribution {


my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1);

for (my $i=0; $i < scalar(@Probabilities); $i++) {
if ( $Probabilities[$i] == 1.0 ) {
$Probabilities[$i] = $P_Consensus;
} else {
$Probabilities[$i] = $P_NonConsensus;
}
}

return();
}

# ==========================================
sub convertToIntervals {

my $Sum = 0;

for (my $i=1; $i < scalar(@Probabilities); $i++) {
$Probabilities[$i] += $Probabilities[$i-1];
}

return();
}

# ==========================================
sub getRandomCharacter {

my ($RandomNumber) = @_;
my $i=0;
for ($i=0; $i < scalar(@Probabilities); $i++) {
if ($Probabilities[$i] > $RandomNumber) { last; }
}

return($Alphabet[$i]);
}
*******************************************************



2nd code
********************************************************
#!/usr/bin/perl

use strict;
use warnings;

my (@short, @long,$x,$r, $output_norm);

open (SHORT, "< short_sequences16_1.txt");
chomp (@short = <SHORT>);
close SHORT;

open (LONG, "< long_sequences.txt");
chomp (@long = <LONG>);
close LONG;

open (OUT_INITIAL, "> output_1.txt");
open (OUT_REPLACED, "> output_2.txt");

for ($x=0; $x<=$#short; $x++) {
$r=int(rand(length ($long[$x]) - length ($short[$x]) + 1));
print OUT_INITIAL ">SeqName$x\n$long[$x]\n";
print OUT_REPLACED "SeqName$x\n" . $r. "\n";
}

close OUT_INITIAL;
close OUT_REPLACED;
********************************************************

 

[TrojanWarBlade]

Everwood!

We're writing all your code for you matey! ;-)



Trojan.

 

[Everwood]

Trojan,

Sorry about that

 

[TrojanWarBlade]

It's ok. Not a problem.
I noticed that many others have been helping you more recently than I have so they will know your code better than I so I'll leave it to them to help finalise it.

I'll check back and if they get really stuck (which I doubt) then I'll poke my nose back in!

Good luck. :-D


Trojan.

 

[Everwood]

Trojan,

Thank you!

 

[KevinADC]

make the second script a sub routine of the first script and call the sub routine when needed. In other words, copy and paste the code of the second script to the bottom of the first script minus this stuff:

#!/usr/bin/perl
use strict;
use warnings;

surround it with brackets and a sub routine name

sub make_files {
my (@short, @long,$x,$r, $output_norm);

open (SHORT, "< short_sequences16_1.txt");
chomp (@short = <SHORT>);
close SHORT;

open (LONG, "< long_sequences.txt");
chomp (@long = <LONG>);
close LONG;

open (OUT_INITIAL,  "> output_1.txt");
open (OUT_REPLACED, "> output_2.txt");

for ($x=0; $x<=$#short; $x++) {
  $r=int(rand(length ($long[$x]) - length ($short[$x]) + 1));
  print OUT_INITIAL ">SeqName$x\n$long[$x]\n";
  print OUT_REPLACED "SeqName$x\n" . $r. "\n";
}

close OUT_INITIAL;
close OUT_REPLACED;
}

and call the make_files sub routine in your main script when needed.

 

[Everwood]

Thanks, Kevin! I will try it soon!

 

[Everwood]

Hi Kevin,

Below is my code for the whole part. Can you
help me check that? The input file is "origin8.txt".

********************************************
CODE

#!/usr/bin/perl
use strict;
use warnings;
my (@origin, $y);
my $N_Sequences = 100;
my @Alphabet = split(//,'ACGT');
my $P_Consensus = 0.85; # This is the #probability of dominant letter
# ====== Globals ==========================
my @Probabilities; # Stores the #probability of each character


# ====== Program ==========================

open (ORIGIN, "< origin8.txt"); # This file holds 200 #sequences used for motif template
chomp (@origin = <ORIGIN>);
close ORIGIN;

for ($y=0; $y<=$#origin; $y++) {


my @Motif = split(//,'$origin[$y]'); # This is a #loop to get the motif template from origin8
open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open file :$!";
for (my $i=0; $i < $N_Sequences; $i++) {
for (my $j=0; $j < scalar(@Motif); $j++) {
loadConsensusCharacter($Motif[$j]);
addNoiseToDistribution();
convertToIntervals();
print OUT_NORM (getRandomCharacter(rand(1.0)));
}
print OUT_NORM "\n";
make_files();
}
}

exit();

# ====== Subroutines =======================
#
sub loadConsensusCharacter {
my ($char) = @_;
my $Found = 'FALSE';

for (my $i=0; $i < scalar(@Alphabet); $i++) {
if ( $char eq $Alphabet[$i]) {
$Probabilities[$i] = 1.0;
$Found = 'TRUE';
} else {
$Probabilities[$i] = 0.0;
}
}
if ($Found eq 'FALSE') {
die("Panic: Motif-Character\"$char\" was not found in Alphabet.
Aborting.\n");
}

return();
}

# ==========================================
sub addNoiseToDistribution {


my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1);

for (my $i=0; $i < scalar(@Probabilities); $i++) {
if ( $Probabilities[$i] == 1.0 ) {
$Probabilities[$i] = $P_Consensus;
} else {
$Probabilities[$i] = $P_NonConsensus;
}
}

return();
}

# ==========================================
sub convertToIntervals {

my $Sum = 0;

for (my $i=1; $i < scalar(@Probabilities); $i++) {
$Probabilities[$i] += $Probabilities[$i-1];
}

return();
}

# ==========================================
sub getRandomCharacter {

my ($RandomNumber) = @_;
my $i=0;
for ($i=0; $i < scalar(@Probabilities); $i++) {
if ($Probabilities[$i] > $RandomNumber) { last; }
}

return($Alphabet[$i]);
}

# ==========================================
sub make_files {
my (@short, @long,$x,$r, $output_norm);

open (SHORT, "< short_sequences8_[$y].txt");
chomp (@short = <SHORT>);
close SHORT;

open (LONG, "< long_sequences.txt");
chomp (@long = <LONG>);
close LONG;

open (OUT_INITIAL, "> output_1.txt");
open (OUT_REPLACED, "> output_2.txt");

for ($x=0; $x<=$#short; $x++) {
$r=2;
print OUT_INITIAL ">SeqName$x\n$long[$x]\n";
print OUT_REPLACED "SeqName$x\n" . substr($long[$x], $r, length $short[$x]) . "\n";}


close OUT_INITIAL;
close OUT_REPLACED;

******************************************************

origin8.txt

******************
TTTATAAT
TGTCAATG
CGTTGATG
CGTCCTAG
GGCTTCCA
ATTAGCCT
GTCCTGAT
TGTAAATC
CGCTTATT
TTGACATA
CCTGATAT
ATGAATCG
CGTCCGAT
TGGCCCAT
ATCCTGAT
TGCCCATT
CCCTAACT
AAAAAAAA
TTTTTTTT
CCCCCCCC
GGGGGGGG
AAAAAAAT
AAAAAAAG
AAAAAAAC
AAAAAACC
AAAAAATT
AAAAAAGG
AAAAAACT
AAAAAACG
AAAAAACA
AAAAACAA
AAAACAAA
AAACAAAA
AACAAAAA
ACAAAAAA
CAAAAAAA
AAAAAATA
AAAAATAA
AAAATAAA
AAATAAAA
AATAAAAA
ATAAAAAA
TAAAAAAA
AAAAAAGA
AAAAAGAA
AAAAGAAA
AAAGAAAA
AAGAAAAA
AGAAAAAA
GAAAAAAA
AAAACCAA
AACCAAAA
CCAAAAAA
AAAATTAA
AATTAAAA
TTAAAAAA
AAAAACCC
AAAACCCA
AAACCCAA
AACCCAAA
ACCCAAAA
CCCAAAAA
AAAAATTT
AAAATTTA
AAATTTAA
AATTTAAA
ATTTAAAA
TTTAAAAA
AAAAAGGG
AAAAGGGA
AAAGGGAA
AAGGGAAA
AGGGAAAA
GGGAAAAA
AAAACCCC
AAACCCCA
AACCCCAA
ACCCCAAA
CCCCAAAA
AAAATTTT
AAATTTTA
AATTTTAA
ATTTTAAA
TTTTAAAA
AAAAGGGG
AAAGGGGA
AAGGGGAA
AGGGGAAA
GGGGAAAA
AAACCCCC
AACCCCCA
ACCCCCAA
CCCCCAAA
AAATTTTT
AATTTTTA
ATTTTTAA
TTTTTAAA
AAAGGGGG
AAGGGGGA
AGGGGGAA
GGGGGAAA
AAGGGGGG
AGGGGGGA
GGGGGGAA
AACCCCCC
ACCCCCCA
CCCCCCAA
AATTTTTT
ATTTTTTA
TTTTTTAA
ATTTTTTT
TTTTTTTA
ACCCCCCC
CCCCCCCA
AGGGGGGG
GGGGGGGA
ATTTTTTT
TTTTTTTA
ATAAAATA
AATAAATA
AAATAATA
AAAATATA
ACAAAACA
AACAAACA
AAACAACA
AAAACACA
AGAAAAGA
AAGAAAGA
AAAGAAGA
AAAAGAGA
ATAAAAGA
ATAAAACA
AGAAAATA
AGAAAACA
ACAAAAGA
ACAAAATA
ATTAAATA
AATTAATA
AAATTATA
ACCAAACA
AACCAACA
AAACCACA
AGGAAAGA
AAGGAAGA
AAAGGAGA
ATTTAATA
AATTTATA
ACCCAACA
AACCCACA
AGGGAAGA
AAGGGAGA
ATTTAACA
ATTTAAGA
AATTTACA
AATTTAGA
ACCCAATA
ACCCAAGA
AACCCATA
AACCCAGA
AGGGAACA
AGGGAATA
AAGGGATA
AAGGGACA
TTGGGACA
CCGGGACA
AGAAGGGA
TGCCCATA
TAAAAAAT
TGCCTATA
CCGTAGTC
ACTTGACT
CTGATCCC
TGTGACTA
CCTGATCC
CCTGAACC
TGATCACG
GGGTAACC
CTTTTGAA
TTGTATGA
CCTGATAA
CTGGTTAG
CCCCGACC
TTGGGGAC
GGTTTGAC
GCTTAGAC
GTTACACC
TTGTACCA
TGGTACCA
CCGTACAT
CCCTTGCC
GTGTTGGT
ATCGATCG
ACGTACGT
TCAGTCAG
GCTATACG
GTCCATAC
CCGTCCGT
ATATATCC
GTGTCCCC

******************

 

[Everwood]

Hi Kevin,

(1)There should be a "}" at the end of the code which I missed that.

(2)The error message I got is:

"Panic: Motif-Character"$" was not found in Alphabet.
Aborting."

What is your idea? I appreciate!

 

[Everwood]

Hi Kevin,

I changed the code

my @Motif = split(//,'$origin[$y]'); # This is a loop to #get the motif template from origin8

to

my @Motif = split(//,$origin[$y]); # This is a loop to #get the motif template from origin8

which solved the error message.

But I ended up with getting 200 "short_sequences8_[$y].txt" files which I did NOT want.

I guess there was sth wrong with calling the subroutine "make_file". Can you suggest me on that?

Thanks,

Alex

 

[Everwood]

Hi! I found the problem and changed the codes in Subroutine "make_file" to

open (OUT_INITIAL, "> output8_[$y]1.txt");
open (OUT_REPLACED, "> output8_[$y]2.txt");

Then this code can generate 200 output8_[$y]1.txt files
and 200 output8_[$y]2.txt which I need.

However, neither of these files holds any sequences. Anybody can suggest me?

Thanks,

 

[Everwood]

Hi all,


The updated code is :


#!/usr/bin/perl
use strict;
use warnings;
my (@origin, $y);
my $N_Sequences = 100;
my @Alphabet = split(//,'ACGT');
my $P_Consensus = 0.85; # This is the probability of dominant letter
# ====== Globals ==========================
my @Probabilities; # Stores the probability of each character


# ====== Program ==========================

open (ORIGIN, "< origin8.txt"); # This file holds 200 sequences used for motif template
chomp (@origin = <ORIGIN>);
close ORIGIN;

for ($y=0; $y<=$#origin; $y++) {


my @Motif = split(//,'$origin[$y]'); # This is a loop to get the motif template from origin8
open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open file :$!";
for (my $i=0; $i < $N_Sequences; $i++) {
for (my $j=0; $j < scalar(@Motif); $j++) {
loadConsensusCharacter($Motif[$j]);
addNoiseToDistribution();
convertToIntervals();
print OUT_NORM (getRandomCharacter(rand(1.0)));
}
print OUT_NORM "\n";
make_files();
}
}

exit();

# ====== Subroutines =======================
#
sub loadConsensusCharacter {
my ($char) = @_;
my $Found = 'FALSE';

for (my $i=0; $i < scalar(@Alphabet); $i++) {
if ( $char eq $Alphabet[$i]) {
$Probabilities[$i] = 1.0;
$Found = 'TRUE';
} else {
$Probabilities[$i] = 0.0;
}
}
if ($Found eq 'FALSE') {
die("Panic: Motif-Character\"$char\" was not found in Alphabet.
Aborting.\n");
}

return();
}

# ==========================================
sub addNoiseToDistribution {


my $P_NonConsensus = ( 1.0-$P_Consensus) / (scalar(@Alphabet) - 1);

for (my $i=0; $i < scalar(@Probabilities); $i++) {
if ( $Probabilities[$i] == 1.0 ) {
$Probabilities[$i] = $P_Consensus;
} else {
$Probabilities[$i] = $P_NonConsensus;
}
}

return();
}

# ==========================================
sub convertToIntervals {

my $Sum = 0;

for (my $i=1; $i < scalar(@Probabilities); $i++) {
$Probabilities[$i] += $Probabilities[$i-1];
}

return();
}

# ==========================================
sub getRandomCharacter {

my ($RandomNumber) = @_;
my $i=0;
for ($i=0; $i < scalar(@Probabilities); $i++) {
if ($Probabilities[$i] > $RandomNumber) { last; }
}

return($Alphabet[$i]);
}

# ==========================================
sub make_files {
my (@short, @long,$x,$r, $output_norm);

open (SHORT, "< short_sequences8_[$y].txt");
chomp (@short = <SHORT>);
close SHORT;

open (LONG, "< long_sequences.txt");
chomp (@long = <LONG>);
close LONG;

open (OUT_INITIAL, "> output8_[$y]1.txt");
open (OUT_REPLACED, "> output8_[$y]2.txt");

for ($x=0; $x<=$#short; $x++) {
$r=2;
print OUT_INITIAL ">SeqName$x\n$long[$x]\n";
print OUT_REPLACED "SeqName$x\n" . substr($long[$x], $r, length $short[$x]) . "\n";}


close OUT_INITIAL;
close OUT_REPLACED;

}

 

[Everwood]

Hi all,

I am able to get files:

short_sequences8_[$y].txt

as well as

output8_[$y]1.txt
output8_[$y]2.txt

short_sequences8_[$y].txt does hold the sequences which I
want but neither output8_[$y]1.txt or output8_[$y]2.txt holds
any sequences. I guess the problem is caused by a failure of
passing data to the subroutine make_file ().

Can anybody give me some advice?

Thank you!

 

[KevinADC]

post the origin8.txt file and maybe someone will check for you. Without that file it's hard to run your code and see what's going on. Your code is hard to read anyway, all those (i=0; i< $blah;i++) loops make my head spin.

 

[Everwood]

Hi Kevin,

Sorry to bother you again . I am attaching my
origin8.txt file here (actually I did that but
you did not noticed).

Thanks a lot.......

Alex







******************
origin8.txt


TTTATAAT
TGTCAATG
CGTTGATG
CGTCCTAG
GGCTTCCA
ATTAGCCT
GTCCTGAT
TGTAAATC
CGCTTATT
TTGACATA
CCTGATAT
ATGAATCG
CGTCCGAT
TGGCCCAT
ATCCTGAT
TGCCCATT
CCCTAACT
AAAAAAAA
TTTTTTTT
CCCCCCCC
GGGGGGGG
AAAAAAAT
AAAAAAAG
AAAAAAAC
AAAAAACC
AAAAAATT
AAAAAAGG
AAAAAACT
AAAAAACG
AAAAAACA
AAAAACAA
AAAACAAA
AAACAAAA
AACAAAAA
ACAAAAAA
CAAAAAAA
AAAAAATA
AAAAATAA
AAAATAAA
AAATAAAA
AATAAAAA
ATAAAAAA
TAAAAAAA
AAAAAAGA
AAAAAGAA
AAAAGAAA
AAAGAAAA
AAGAAAAA
AGAAAAAA
GAAAAAAA
AAAACCAA
AACCAAAA
CCAAAAAA
AAAATTAA
AATTAAAA
TTAAAAAA
AAAAACCC
AAAACCCA
AAACCCAA
AACCCAAA
ACCCAAAA
CCCAAAAA
AAAAATTT
AAAATTTA
AAATTTAA
AATTTAAA
ATTTAAAA
TTTAAAAA
AAAAAGGG
AAAAGGGA
AAAGGGAA
AAGGGAAA
AGGGAAAA
GGGAAAAA
AAAACCCC
AAACCCCA
AACCCCAA
ACCCCAAA
CCCCAAAA
AAAATTTT
AAATTTTA
AATTTTAA
ATTTTAAA
TTTTAAAA
AAAAGGGG
AAAGGGGA
AAGGGGAA
AGGGGAAA
GGGGAAAA
AAACCCCC
AACCCCCA
ACCCCCAA
CCCCCAAA
AAATTTTT
AATTTTTA
ATTTTTAA
TTTTTAAA
AAAGGGGG
AAGGGGGA
AGGGGGAA
GGGGGAAA
AAGGGGGG
AGGGGGGA
GGGGGGAA
AACCCCCC
ACCCCCCA
CCCCCCAA
AATTTTTT
ATTTTTTA
TTTTTTAA
ATTTTTTT
TTTTTTTA
ACCCCCCC
CCCCCCCA
AGGGGGGG
GGGGGGGA
ATTTTTTT
TTTTTTTA
ATAAAATA
AATAAATA
AAATAATA
AAAATATA
ACAAAACA
AACAAACA
AAACAACA
AAAACACA
AGAAAAGA
AAGAAAGA
AAAGAAGA
AAAAGAGA
ATAAAAGA
ATAAAACA
AGAAAATA
AGAAAACA
ACAAAAGA
ACAAAATA
ATTAAATA
AATTAATA
AAATTATA
ACCAAACA
AACCAACA
AAACCACA
AGGAAAGA
AAGGAAGA
AAAGGAGA
ATTTAATA
AATTTATA
ACCCAACA
AACCCACA
AGGGAAGA
AAGGGAGA
ATTTAACA
ATTTAAGA
AATTTACA
AATTTAGA
ACCCAATA
ACCCAAGA
AACCCATA
AACCCAGA
AGGGAACA
AGGGAATA
AAGGGATA
AAGGGACA
TTGGGACA
CCGGGACA
AGAAGGGA
TGCCCATA
TAAAAAAT
TGCCTATA
CCGTAGTC
ACTTGACT
CTGATCCC
TGTGACTA
CCTGATCC
CCTGAACC
TGATCACG
GGGTAACC
CTTTTGAA
TTGTATGA
CCTGATAA
CTGGTTAG
CCCCGACC
TTGGGGAC
GGTTTGAC
GCTTAGAC
GTTACACC
TTGTACCA
TGGTACCA
CCGTACAT
CCCTTGCC
GTGTTGGT
ATCGATCG
ACGTACGT
TCAGTCAG
GCTATACG
GTCCATAC
CCGTCCGT
ATATATCC
GTGTCCCC

 

[KevinADC]

first thing is you have an "error" here:

my @Motif = split(//,'$origin[$y]');

you surrounded $origin[$y] with single quotes which is killing the variable interpolation, remove the single quotes:

my @Motif = split(//,$origin[$y]);

I did that and ran the code and got what you got:

short_sequences8_[$y].txt does hold the sequences which I
want but neither output8_[$y]1.txt or output8_[$y]2.txt holds any sequences.

Then I noticed in your main loop you are writing to this file: short_sequences8_[$y].txt

and in the make_file() sub you are trying to read from the same file:

open (SHORT, "< short_sequences8_[$y].txt");

during the same loop through your main loop, this just can't be correct I thought. So I changed the main loop from this:

for ($y=0; $y<=$#origin; $y++) {
  

    my @Motif = split(//,'$origin[$y]');     # This is a loop to get the motif template from origin8
    open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open file :$!";
        for (my $i=0; $i < $N_Sequences; $i++) {
            for (my $j=0; $j < scalar(@Motif); $j++) {
                 loadConsensusCharacter($Motif[$j]);    
                 addNoiseToDistribution();             
                 convertToIntervals();
                 print OUT_NORM (getRandomCharacter(rand(1.0)));
            }
            print OUT_NORM "\n";
            make_files();
        }
}

exit();

to this:

for ($y=0; $y<=$#origin; $y++) {
    my @Motif = split(//,$origin[$y]);     # This is a loop to get the motif template from origin8
    open (OUT_NORM, ">short_sequences8_[$y].txt") or die "Unable to open file :$!";
    for (my $i=0; $i < $N_Sequences; $i++) {
        for (my $j=0; $j < scalar(@Motif); $j++) {
             loadConsensusCharacter($Motif[$j]);    
             addNoiseToDistribution();             
             convertToIntervals();
             print OUT_NORM (getRandomCharacter(rand(1.0)));
        }
        print OUT_NORM "\n";
    }
    close OUT_NORM;
    make_files();
}
exit();

and I reduced the $N_sequences to 2 to test it out. Now with just 2 loops to test the script, the script produced 198 files for output8_[n]1.txt, output_[n]2.txt and short_sequences8_[n].txt. All the files were populated with data although I am not sure it's the correct data. But if you were to run the script through 100 loops it's going to produce a tremendous amount of files and take a long time to run, is that what you are expecting?

 

[Everwood]

Hi Kevin,

Thank you so much and I appreciate it!


(1)You mentioned an error here:
******************************************************
my @Motif = split(//,'$origin[$y]');

you surrounded $origin[$y] with single quotes which is killing the variable interpolation, remove the single quotes:

my @Motif = split(//,$origin[$y]);"
******************************************************
I already noticed that and changed the error. Thanks for mentioning it.

(2)In addition to (1), I found another change is that you put "close OUT_NORM;" right before "make_files();"

Now I test it and find at least all output8_[n]1.txt, output_[n]2.txt and short_sequences8_[n].txt files holds data. That is very close to what I want although I have not check data.

I guess "close OUT_NORM;" is what I missed.




Thank you so much!

Alex

 

[Everwood]

Hi Kevin,

I have reviewed the data generated.

(1)I get 200 short_sequences8_[n].txt files n=[0..199]

I find that:
short_sequences8_[0].txt..short_sequences8_[99].txt containes
the right data;

short_sequences8_[100]..short_sequences8_[198].txt do have data but they are wrong;

short_sequences8_[199].txt is empty.

(2)Since the input files to the subroutine "make_file()" are almost wrong so there is no wonder that the final results are messed up.


I guess there is still some problem with the loop. How do you think?

Thank you very much! I am grateful to your help!

Alex

 

[KevinADC]

I really have no idea what the final output should be so it's difficult to know what the problem might be. You have so many loops it makes my head dizzy trying to figure out what is going on in the script. Personally, I think you should be trying to build a data set and printing the data set to file after everything is done, but that could mean starting over almost from scratch (from the beginning). I may take another stab at it later, but hopefully someone else will want the challenge of debugging your script.