Sliding window perl program

genome has asked for the wisdom of the Perl Monks concerning the following question:

I have two input files :-

File 1

CTSC    chr11    -    650    E    RAB38    chr11    -    87883123    E
+    12    2    INTRACHR-SS-OGO-0GAP    inframe-shift

file 2 

chr11    602    63889087    HWI-ST216_106:3:67:14628:181851    -
chr11    613    69889087    HWI-ST216_106:3:24:16406:176388    +
chr11    614    80889087    HWI-ST216_106:3:21:13731:105239    +
chr11    643    94888888    HWI-ST216_111:5:22:3149:116167    +
chr11    678    98889079    HWI-ST216_106:3:5:18058:57952    +
chr11    612    108888887    HWI-ST216_106:3:8:5578:44855    +
chr5    612    63889087    HWI-ST216_106:3:67:14628:181851    -
chr3    88033200    69889087    HWI-ST216_106:3:24:16406:176388    +
chr2    88033345    80889087    HWI-ST216_106:3:21:13731:105239    +
chr1    88033376    94888888    HWI-ST216_111:5:22:3149:116167    +
chr6    88034000    98889079    HWI-ST216_106:3:5:18058:57952    +
chr7    88034123    108888887    HWI-ST216_106:3:8:5578:44855    +
[download]

I want to count the number of entries in the second column of second file within 500+ (up) and 500- (down) to the number medntioned in the second column of first file.

For this, I made an script, but does not giving the desired result:-

#!/usr/bin/perl -w

$file1=$ARGV[0];    #First file 
$file2=$ARGV[1];    #second file 
open(TR,$file1); 
while ($line1=<TR>) 
{
chomp($line1);
@ar1 = split(/\t/,$line1);
chomp($ar1[1]);chomp($ar1[3]);
$up = $ar1[3]-500;
$dn = $ar1[3]+500; 
open(SC,$file2);
while ($line2=<SC>)
{
    chomp($line2);
    @array2 = split (/\t/, $line2);
    if ($ar1[1] eq $array2[0])
    {
for ($mm=$up;$mm<=$dn;$mm+=100)
{
$gt = $up+100;
$c ='0';    
if (($array2[1]> $up) && ($array2[1] < $gt)) 
{

    print "$up\t$gt\t$array2[1]\n";
    $c++;
}

$up=$up+50;
        
} 

}
    
    }
    
}
[download]

Result produced is

550    650    602 <p>
600    700    602 <p>
[download]

But where is the count of 612,613, 614 etc.. these numbers are in the rage.

Comment on Sliding window perl program Select or Download Code

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Re: Sliding window perl program by GotToBTru (Prior) on Oct 20, 2015 at 19:51 UTC
You've been here before. Using <c> tags is not that hard. Update: You are incrementing $up within the for loop within the while loop, so you aren't comparing the range you think you are after the first $file2. You probably want to set the value of $up before the for loop. Further Update: much more readable! I see my guesses about the code were correct. If you can properly indent it as well, the structure of the code will become clearer, and that's to your benefit; it will be easier to see why it does not work. BTW: variable $c has no apparent purpose. You set it to zero, and then conditionally increment it, only to zero it again next range. Dum Spiro Spero	[reply]
Re^2: Sliding window perl program by genome (Novice) on Oct 20, 2015 at 20:15 UTC
Please have a look now.	[reply]
Re^3: Sliding window perl program by hippo (Archbishop) on Oct 20, 2015 at 21:42 UTC
Just for fun, I did. Here's what happened: $ perl -cw 1145471.pl Unquoted string "p" may clash with future reserved word at 1145471.pl +line 6. Scalar found where operator expected at 1145471.pl line 11, near "$up" (Missing semicolon on previous line?) Scalar found where operator expected at 1145471.pl line 12, near "$dn" (Missing semicolon on previous line?) Scalar found where operator expected at 1145471.pl line 23, near "$c" (Missing semicolon on previous line?) Unquoted string "p" may clash with future reserved word at 1145471.pl +line 24. Scalar found where operator expected at 1145471.pl line 31, near "$up" (Missing semicolon on previous line?) syntax error at 1145471.pl line 6, near "p>" syntax error at 1145471.pl line 10, near "chomp" syntax error at 1145471.pl line 11, near "$up " syntax error at 1145471.pl line 15, near ") {" syntax error at 1145471.pl line 19, near ") {" syntax error at 1145471.pl line 21, near "100) " syntax error at 1145471.pl line 24, near ") <" syntax error at 1145471.pl line 29, near "}" syntax error at 1145471.pl line 33, near "}" 1145471.pl had compilation errors. [download] Do you see the problem?	[reply] [d/l]
Re: Sliding window perl program by Laurent_R (Canon) on Oct 20, 2015 at 20:57 UTC
Untested code illustrating the algorithm described in my post above: `# opening file 1 # ... my %hash; while (my $line1=<TR>) { chomp($line1); my @ar = split(/\t/,$line1); $hash{$ar[1]} = $ar[3]; } close TR; open my $SC, "<", $file2 or die "Error blah blah... $!"; while (my $line2 = <$SC>) { my ($id, $val) = split /\t/, $line2; my $val_file1 = $hash{$id}; if ( $val > $val_file1 - $margin and $val < $val_file1 + $margin) +{ # print out something } } close $SC;` [download] BTW, I basically kept your syntax almost unchanged for the first part and tried to improve it in accordance to good practices in the second part. Take a look at the differences.	[reply] [d/l]
Re^2: Sliding window perl program by genome (Novice) on Oct 21, 2015 at 18:02 UTC
Hi, This program is for sliding window. I want to count the number of entries of file 2 , lies between the variable range (100 size window with 50 size slid) of sliding window from +500 to the -500 of 650. That is because I put a for loop of 100 increment and then tries to increase the $up number 50. i.e. 150-250 200-300 250-350 ... ... ... 1100-1150 I hope u understand the question.	[reply]
Re^3: Sliding window perl program by Laurent_R (Canon) on Oct 21, 2015 at 23:18 UTC
Well, since you insist on sliding windows, it appears that I missed your requirement, sorry about that. But I still really don't understand what you want. Perhaps a more detailed example of your input and desired output would help.	[reply]
Re^4: Sliding window perl program by genome (Novice) on Oct 22, 2015 at 14:27 UTC
Re^5: Sliding window perl program by Laurent_R (Canon) on Oct 22, 2015 at 18:56 UTC
Re^5: Sliding window perl program by Laurent_R (Canon) on Oct 22, 2015 at 21:20 UTC
Re: Sliding window perl program by Laurent_R (Canon) on Oct 20, 2015 at 20:37 UTC
Your file 1 has only one line. Is this going to be the case with your real data? If yes, you only need to pick up the lines of file 2 where column two falls between the range defined by file 1. But if file 1 has several lines, then you need to explain how to do the match between the two files. From looking at your data, maybe you want this: for each line in file 1, check the ID (e.g. chr11) in the second field, pick up the pivot value in the 4th field (650), and grab in file 2 all lines whose ID is chr11 and whose second field is within the range (650-500..650+500). If this is what you want, I suggest that you should read the full file 1 and store ID/4th field of each line in a hash. Close File 1. Read file 2, for each line in file 2, check the ID, lookup the pivot value for this ID in the hash, and check if field 2 falls within the range.	[reply]
Re: Sliding window perl program by LanX (Saint) on Oct 20, 2015 at 19:51 UTC
I have problems to read your post on my mobile, but maybe this is what you are looking for? Re: Memory Leak when slurping files in a loop (sliding window explained) Cheers Rolf _{(addicted to the Perl Programming Language and ☆☆☆☆ :) Je suis Charlie!}	[reply]
Re^2: Sliding window perl program by genome (Novice) on Oct 20, 2015 at 20:14 UTC
Its not the question. I have corrected the code. Please have a look now.	[reply]
Re^3: Sliding window perl program by u65 (Chaplain) on Oct 20, 2015 at 20:37 UTC
I'm afraid your code corrections are incomplete: spurious "<c>" and "<p>" tags all over the place inside the main code block badly formatted code, e.g., inconsistent indentation (perhaps caused by the spurious tags)	[reply]