while loop - Using perl to cycle through a list of values (x) and compare to another file with value ranges -

i have 2 files. 1 file has list of values so

nc_snpstest.txt

250  275  375 

the other file has space delimited information. column 1 first value of range, column 2 has second value of range, column 5 has name of range, , column 8 has acts on range.

promoterstest.txt

20 100 yaax f yaax 5147 5.34 sigma70 99 200 300 yaaa r yaaap1 6482 6.54 sigma70 35 350 400 yaaa r yaaap2 6498 2.86 sigma70 51 

i trying write script takes first line file 1 , parses file 2 line line see if value falls in range between first 2 columns.

when first match found, want print value file 1 , values in file 2 columns 5 , 8 line match. if no match found in file 2 print value file 1 , move on.

it seems should simple enough task i'm having issue cycling though both files.

this have written:

#!/usr/bin/perl  use warnings; use strict;  open $promoterfile, '<', 'promoterstest.txt' or die $!; open $snpsfile, '<', 'nc_snptest.txt' or die $!;  open (file, ">promotermatchtest.txt");  while (my $snps = <$snpsfile>) {    chomp ($snps);     while (my $cord = <$promoterfile>) {       chomp ($cord);        @cordfile =split(/\s/, $cord);        $lend = $cordfile[0];       $rend = $cordfile[1];       $promoter = $cordfile[4];       $sigmafactor = $cordfile[7];        foreach $a ($snps)        {          if ($a >= $lend && $a <= $rend)          {             print file "$a\t$cordfile[4]\t$cordfile[7]\n";          }          else           {              print file "$a\n";          }       }    } } close file; close $promoterfile; close $snpsfile; exit; 

so far output looks so:

250 250     yaaap1  sigma70 250 

where first line of file 1 being called , file 2 being cycled through. else command being used on each line of file 2 , script never cycles through other lines of file 1.

your problem you're not resetting progress through second file. read 1 line $snpsfile, check against ever line in second file.

but when start over, you're @ end of file, so:

while (my $cord = <$promoterfile>) { 

doesn't have read.

a quick fix add seek command in there, that'll make inefficient code. i'd suggest instead reading file 1 array, , referencing instead.

here's first draft rewrite may help.

#!/usr/bin/perl  use warnings; use strict;  use data::dumper;  open $promoterfile, '<', 'promoterstest.txt'     or die $!; open $snpsfile,     '<', 'nc_snptest.txt'        or die $!; open $output,       ">", "promotermatchtest.txt" or die $!;   @data;  while (<$promoterfile>) {     chomp;     @cordfile    = split;     $lend        = $cordfile[0];     $rend        = $cordfile[1];     $promoter    = $cordfile[4];     $sigmafactor = $cordfile[7];      push(         @data,         {   lend        => $cordfile[0],             rend        => $cordfile[1],             promoter    => $cordfile[4],             sigmafactor => $cordfile[7]         }     ); }  print dumper \@data;  foreach $value (<$snpsfile>) {     chomp $value;     $found = 0;     foreach $element (@data) {         if (    $value >= $element->{lend}             , $value <= $element->{rend} )         {             #print "found $value\n";             print {$output} join( "\t",                 $value, $element->{promoter}, $element->{sigmafactor} ),                 "\n";             $found++;             last;         }      }     if ( not $found ) {         print {$output} $value,"\n";     } }  close $output; close $promoterfile; close $snpsfile; 

first - open file2, read in stuff in array of hashes. (if of elements there unique, key off instead.)

then read through snpsfile 1 line @ time, looking each key - printing if exists (at least once, on first hit) , printing key if doesn't.

this generates output:

250     yaaap1  sigma70 275     yaaap1  sigma70 375     yaaap2  sigma70 

was aiming for?

aside 'dumper' statement outputs content of @data thus:

$var1 = [           {             'sigmafactor' => 'sigma70',             'promoter' => 'yaax',             'lend' => '20',             'rend' => '100'           },           {             'sigmafactor' => 'sigma70',             'promoter' => 'yaaap1',             'rend' => '300',             'lend' => '200'           },           {             'promoter' => 'yaaap2',             'sigmafactor' => 'sigma70',             'rend' => '400',             'lend' => '350'           }         ];