How to get a while loop to recognize an extracted number

[sessmurda]

I am writing a fairly simple script that is supposed to print out lines from a txt file and group them based on where I want them. The general format of the files I am using the script on is as follows:

662376 [S] |GCGG | | |
662375 [S] |CGCC | | |
662374 [S] |GCGG | | |
662373 [H] |CATC | | |
662371 [Y] |TCCC | | |
662369 [M] |CACCC| | |
662367 [Y] |TCTTT| | |
662365 [S] |GCGGG| | |
662364 [R] |AGAAA| | |
662360 [M] |CACCC| | |
662359 [W] |ATAAA| | |
662358 [S] |CGCCC| | |
662357 [M] |ACAAA| | |
662356 [R] |GAAAG| | |
662354 [S] |GCGGG| | |
662353 [R] |AGAAA| | |
662352 [R] |GAGGG| | |
662350 [K] |TGTTT| | |
662349 [Y] |CTCCC| | |
662348 [M] |ACAAA| | |
662347 [R] |GAGGG| | |
662376 [S] |GCGG | | |
662375 [S] |CGCC | | |
662374 [S] |GCGG | | |
662373 [H] |CATC | | |
662371 [Y] |TCCC | | |
662369 [M] |CACCC| | |
662367 [Y] |TCTTT| | |
662365 [S] |GCGGG| | |
662364 [R] |AGAAA| | |
662360 [M] |CACCC| | |
662359 [W] |ATAAA| | |
662358 [S] |CGCCC| | |
662357 [M] |ACAAA| | |
662356 [R] |GAAAG| | |
662354 [S] |GCGGG| | |
662353 [R] |AGAAA| | |
662352 [R] |GAGGG| | |
662350 [K] |TGTTT| | |
662349 [Y] |CTCCC| | |
662348 [M] |ACAAA| | |
662347 [R] |GAGGG| | |


and here is the code:

print "What is the start of the ORF?\n";
$orf_beg = <STDIN>;
 
open (IN, '/home/asession/pracperl/bin/SNPYNR+-1kb.txt') || die "nope\n";
 
while (<IN>) {
 
    chomp;
 
    $position = substr $_, 1, 11;               # extract the position
    $type_of_polymorphism = substr $_, 13, 3;   # extract the polymorphism type, same as ref if no polymorphism
    $ref_seq = substr $_, 17, 1;                # extract the cerevisiae ref sequence
    $para_seq = substr $_, 18, 1;               # extract the paradoxus sequence
    $mika_seq = substr $_, 19, 1;               # extract the mika sequence
    $kudr_seq = substr $_, 20, 1;               # extract the kudr sequence
    $baya_seq = substr $_, 21, 1;               # extract the bayanus sequence
 
 
    $baya_seq =~ s/\s+/x/g;
    #$position =~ tr/ //d;
 
    foreach ($position) {
        while ($postion > $orf_beg) {
        print "$position $ref_seq $para_seq $baya_seq\n";
}}
 
}
close (IN);
 
    print "\n";
 

Basically the problem I am having is that the while loop withing the foreach loop is not recognizing the position variable as a number, I tried to remove the white space, thinking that was an issue, but it did not work. Any suggestions?

[KevinADC]

If this is supposed to be input to the perl program, remove the newline from the end:

print "What is the start of the ORF?\n";

should be:

print "Enter the start of the ORF: ";
chomp($orf_beg = <STDIN>);

[sessmurda]

Thats not the variable that perl isnt recognizing, the $position is the problem, I defined orf beg before opening the file handle so that during the loop it wouldnt ask me to input the start of the ORF before every iteration.

[eWish]

Are you certain that $position has a number in it? Have you checked the value of $position?

--Kevin

[numberwhun]

Are you certain that $position has a number in it? Have you checked the value of $position?

--Kevin

To find out, you could run your script in the Perl debugger and check all the values to make sure. To start the debugger, use:

perl -d <scriptname>
 

THe debugger is a little daunting at first, but its not bad once you read a tutorial, even the one at Perldoc is doable.

Regards,

Jeff

[nithinpes]

Are you certain that $position has a number in it? Have you checked the value of $position?

--Kevin

sessmurda,

I was wondering about the logic in this loop:

    foreach ($position) {
        while ($postion > $orf_beg) {
        print "$position $ref_seq $para_seq $baya_seq\n";
}}
 
 

Inside while ($postion > $orf_beg) {} loop, you are not modifying the value of $position. So, if the condition returns true, this will result in an infinite loop.

You should be using if() loop instead of while(). However, check if $position has indeed a number in it by printing out the value.

- Nithin

[KevinADC]

this line:

$position = substr $_, 1, 11;

with this input fromthe file:

662376 [S] |GCGG | | |

will result in:

62376 [S] |

Is that really what you want?

[numberwhun]

sessmurda,

I was wondering about the logic in this loop:

    foreach ($position) {
        while ($postion > $orf_beg) {
        print "$position $ref_seq $para_seq $baya_seq\n";
}}
 
 

Inside while ($postion > $orf_beg) {} loop, you are not modifying the value of $position. So, if the condition returns true, this will result in an infinite loop.

You should be using if() loop instead of while(). However, check if $position has indeed a number in it by printing out the value.

- Nithin

Also, correct me if I am wrong, but I don't see that $position was defined as an array, so doing a foreach will result in one time through.

Regards,

Jeff

[nithinpes]

Also, correct me if I am wrong, but I don't see that $position was defined as an array, so doing a foreach will result in one time through.

Regards,

Jeff

Thanks for the addition, Jeff. I missed it totally :)

The foreach loop will be of no specific purpose in that section of script.

[sessmurda]

I am currently working on the foreach and while/if suggestions you guys provided, thanks! To answer some questions: the position is a number, it doesnt show when I copy and pasted the text, but there is a lot of white space between the last number of the position and the sequence character to allow for the fact that on occasion there will need to be decimals due to the format of the file. I checked all of the substring column numbers before posting, they are all correct. I originally had the if statement inside the loop but it kept asking me for the polymorphism on every iteration, I incorrectly thought while was what I should be using. Also when I tried pushing the $position variable into an array it would not move past the first position, even when I tried the shift function. When I use the script I posted without the while/if line, and have the $position being acted on by the foreach loop, it works, its just that I want to catalogue the positions based on where I specify it, then output those to each their own file, which I will work on after I get the script working.

Thanks again for the help.