how to write the results to a file in my code? 3

[Everwood]

Hi! My code is to generate 100 sequences (width=8) and print
them on the screen. Now I want to write these sequences to a file and make sure each sequence per a line.

My code is :

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

#!/usr/bin/perl
# randommotifs.pl
use strict;
use warnings;
my $N_Sequences = 100;
my @Motif = split(//,'AGGGGGAA');

my @Alphabet = split(//,'ACTG');
my $P_Consensus = 0.85;

# ====== Globals ==========================
my @Probabilities;
# ====== Program ==========================


for (my $i=0; $i < $N_Sequences; $i++) {
for (my $j=0; $j < scalar(@Motif); $j++) {

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

exit();
*****************************

If I want to store the results in a file named "output.txt",
I should add a line
"open (OUT_NORM, "> output.txt");"
at the beginning of the code, right?

Then it seems that I should add another line
"print OUT_NORM "print OUT_NORM "$long[$x]\n";" into the
"for" loop to substitute
"print (getRandomCharacter(rand(1.0)));
}
print "\n";"

Is my guess right?

Thanks for help!

 

[KevinADC]

try:

open (OUT_NORM, ">output.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)));  
    }
}
close(OUT_NORM);
print "Finished!";

assume that getRandomCharacter(rand(1.0)) is returning the results you want to print to file;

 

[KevinADC]

oops,

add this:

print "\n";

right after:

print OUT_NORM (getRandomCharacter(rand(1.0)));

 

[Everwood]

Hi Kevin,

I used

print OUT_NORM (getRandomCharacter(rand(1.0)));
print "\n";}

and

print OUT_NORM (getRandomCharacter(rand(1.0)));}
print "\n";

neither of them does work. They can generate a
"output.txt" file,which hold all the sequences together like:

GGGGGAAGGGGGTCAAGGGGGAAAGGGGGAAAGGGGTAAGGGGGGAAAGGGCGATAGGGGGAAAGGGGGCAAGGGGGAAAAAGGGAATGGTGGAAAGGGGGAAAGGGCGAAAGGGGTAAAGTGGGAAAGGGAGAAAGGGGGAAAGGGAGAAAGGGGGAAAGGGAGAAAGAGGGAAGGGGGCAAAGGGGGGAAGGGTGAAAGGGGGATGGGAGGAAAGGGGGAGCGGGGGAAAGGGGGAGAGGGGGAGACGGGGAAATGGGGAAACGGGATAAGGGGTAAAGGGAGACAGGGGGACAAGGAAAAACGGGGATAGGAGGAAAGGGTCAATGGGGGAAGGGGGTAAAGGGGGCAATGGGAAAAGCCGGAAAGGCGGAAAGGGGGAAAGGGTGAAATGGAGAAAGGGGGAAAGGGGGAAAGGGGGAGAGGTGGCGAGGTGGATAGCGGGAAAGTGGGAAAGGGGGTAAGGGTGATAGGCGGAAAGGATCAAAGGGGTAAAGGGGGAATGGGGGAAAGGGTGAAGGGGGGAAAGGGGGAAAGGGGGGAAGGGGGAAAGGGGGCAAGGGGGAATGGGGTACAGTGGCACAGGGGAAAAGGGGGAAAGGGGGAGAGCGGTGCAGGGGTCAAGGGGGAAAGGGGGAAAGTGGGAGATGGTGAAAGGGGGCAAGCGGGAAAGGGGGAACGGGGGAAAGGGGGAAAGGGGGAAAGGGGTATAGGGGGAATGGTAAGAAGGGGGGAAGGGGGAAAGGGGGAACGGGTGCAAGGGGCCCAGGACAGAAGCAGTAAAGGGGGAAAGGGGGAAA



Ideally, I want it to be:

GGGGGAAG
GGGGTCAA
etc...


Thanks,

 

[duncdude]

Hi Everwood

I think there is a good chance here that you text file is NOT IN UNIX format - maybe it is in DOS format

Please check it!

I could also be talking rubbish...


Kind Regards
Duncan

 

[duncdude]

i.e. this is what happens if i append to a DOS text file with Perl using "\n":-

line1
line2
line3
new line 1?new line 2?new line 3


Kind Regards
Duncan

 

[Everwood]

hi Duncan,

I also checked the txt file on a linux server...

 

[Everwood]

but it looks the same

 

[Everwood]

any other suggestions?

thanks!

 

[ishnid]

Change
print "\n";

to
print OUT_NORM "\n";

 

[Everwood]

ishnid,thanks! that works!

great!

 

[duncdude]

Oh my god... i am not paying attention am i !!!


Kind Regards
Duncan

 

[Everwood]

duncan,that's oK! thank you so much!

 

[KevinADC]

Change
print "\n";

to
print OUT_NORM "\n";

Thanks ishind!