Sir / Madam,
I would like to map and extract common numbers between 5 column (i.e.Start) and 6th column (End) for refFlat table with 2nd column (Start) and 3rd column (End) for mirna table. Could you please modify the script attach here. I would be glad for your support.

With regards,
Rocky
Seoul, Korea


This is a simple script to extract Start and End column.

#!/usr/bin/perl

use strict;
use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";
my $sql;

$sql = "select * from mirna limit 10";

my $sth = $dbh->prepare($sql);
$sth->execute || die "Error! : $sql\n";

while( my $mirna= $sth->fetchrow_hashref() ){

   my $start = $mirna->{'Start'};
   my $end = $mirna->{'End'};
  
   print "$chr\t$start\t$end\n";
#!/usr/bin/perl

use strict;
use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";
my $sql;

$sql = "select * from mirna, refFlat limit 10";

my $sth = $dbh->prepare($sql);
$sth->execute || die "Error! : $sql\n";

while( my $mirna && $refFlat = $sth->fetchrow_hashref() ){

   my $chr = $mirna->{'chr'};
   my $start = $mirna->{'Start'};
   my $end = $mirna->{'End'};

   my $chr = $refFlat->{'chr'};
   my $start = $refFlat->{'Start'};
   my $end = $refFlat->{'End'};
   
   print "$chr\t$start\t$end\n";
}

Sir/ Madam,

I would like to compare columns in tables in mysql database. From dbsnp table start and end columns with mirna table start and end. These are genomic positions in chromosome. I would like to extract common START and END positions by reading row by row. I have written a script attach here . Could you please modify this error.

#!/usr/bin/perl

use strict;
use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";

my $sql;

$sql = "select d.chr, m.Start as m_start, m.End as m_end, d.Start as d_start, d.End as d_end from mirna as m, dbsnp as d limit 10000";
my $sql1 = "select * from mirna limit 10";
my $sql2 = "select * from dbsnp limit 10";


my $sth = $dbh->prepare($sql);

my $sth1 = $dbh->prepare($sql1);
my $sql1 = "select * from mirna limit 10";
my $sql2 = "select * from dbsnp limit 10";


my $sth = $dbh->prepare($sql);

my $sth1 = $dbh->prepare($sql1);
my $sth2 = $dbh->prepare($sql2);

$sth1->execute || die "Error! : $sql\n";
$sth2->execute || die "Error! : $sql\n";

$sth->execute || die "Error! : $sql\n";

while ( my $line1 = $sth1->fetchrow_hashref() ) {
       while ( my $line2 = $sth2->fetchrow_hashref() ) {
               if ( $line2->{'Start'} <= $line1->{'Start'} && $line1->{'End'} <= $line2->{'End'} ) {
                       print "test";
               }
       }
}

Regards,

Rocky

Seoul National University


[1]: http://i.stack.imgur.com/y8a4P.png

Please attach your data as *.txt file(s) instead of images or *.pdf files. Instead of having to look at the images and manually enter your data into MySQL we could copy and paste it to try and reproduce the error.

Hello,
I would like to map and extract common numbers between 5 column (i.e.Start) and 6th column (End) for refFlat table with 2nd column (Start) and 3rd column (End) for mirna table. I can run this script but I could not map Start and End columns in pre-mirna AND refFlat text files and extract the common with the Start and End columns.

#!/usr/bin/perl

use strict;
use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";

my $sql;

$sql = "select ref.chr, m.Start as m_start, m.End as m_end, ref.Start as ref_start, ref.End as ref_end from mirna as m, refFlat as ref limit 10";
#my $sql1 = "select * from mirna limit 10";
#my $sql2 = "select * from dbsnp limit 10";


my $sth = $dbh->prepare($sql);

#my $sth1 = $dbh->prepare($sql1);
#my $sth2 = $dbh->prepare($sql2);

#$sth1->execute || die "Error! : $sql\n";
#$sth2->execute || die "Error! : $sql\n";

$sth->execute || die "Error! : $sql\n";

#while ( my $line1 = $sth1->fetchrow_hashref() ) {
#       while ( my $line2 = $sth2->fetchrow_hashref() ) {
#               if ( $line2->{'Start'} <= $line1->{'Start'} && $line1->{'End'} <= $line2->{'End'} ) {
#                       print "test";
#               }
#       }
#}


while( my $refFlat = $sth->fetchrow_hashref() ){


  my $chr = $refFlat->{'chr'};
  my $m_start = $refFlat->{'m_start'};
  my $ref_start = $refFlat->{'ref_start'};
  my $m_end = $refFlat->{'m_end'};
  my $ref_end = $refFlat->{'ref_end'};
   # to do~ comparison code~ if(

  print "$chr\t$m_start\t$m_end\t$ref_start\t$ref_end\n";
}

Try moving the statement that executes $sth2 into the outer loop, something like the following (not tested):

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

use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";

my $sql;

$sql = "select d.chr, m.Start as m_start, m.End as m_end, d.Start as d_start, d.End as d_end from mirna as m, dbsnp as d limit 10000";
my $sql1 = "select * from mirna limit 10";
my $sql2 = "select * from dbsnp limit 10";


my $sth = $dbh->prepare($sql);
my $sth1 = $dbh->prepare($sql1);
my $sth2 = $dbh->prepare($sql2);

$sth1->execute || die "Error! : $sql\n";

$sth->execute || die "Error! : $sql\n";

while ( my $line1 = $sth1->fetchrow_hashref() ) {
    $sth2->execute || die "Error! : $sql\n";#Moved into loop
    while ( my $line2 = $sth2->fetchrow_hashref() ) {
        if ( $line2->{'Start'} <= $line1->{'Start'} && $line1->{'End'} <= $line2->{'End'} ) {
                print "test";
        }
    }
}

Dear Sir,

I ran this perl script but there was a error while running it. The output comes like --

[haojamrocky@melon hg18]$ perl test2.pl
Global symbol "$chr" requires explicit package name at test2.pl line 32.
Global symbol "$m_start" requires explicit package name at test2.pl line 32.
Global symbol "$m_end" requires explicit package name at test2.pl line 32.
Global symbol "$d_start" requires explicit package name at test2.pl line 32.
Global symbol "$d_end" requires explicit package name at test2.pl line 32.
Execution of test2.pl aborted due to compilation errors.

I would be happy to see your help.

Regards,
Rocky

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

use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";

my $sql;

$sql = "select d.chr, m.Start as m_start, m.End as m_end, d.Start as d_start, d.End as d_end from mirna as m, dbsnp as d limit 10000";
my $sql1 = "select * from mirna";
my $sql2 = "select * from dbsnp";


my $sth = $dbh->prepare($sql);
my $sth1 = $dbh->prepare($sql1);
my $sth2 = $dbh->prepare($sql2);

$sth1->execute || die "Error! : $sql\n";

$sth->execute || die "Error! : $sql\n";

while ( my $line1 = $sth1->fetchrow_hashref() ) {
    $sth2->execute || die "Error! : $sql\n";#Moved into loop
    while ( my $line2 = $sth2->fetchrow_hashref() ) {
        if ( $line2->{'Start'} <= $line1->{'Start'} && $line1->{'End'} <= $line2->{'End'} ) {
                print "$chr\t$m_start\t$m_end\t$d_start\t$d_end\n";
        }
    }
}

Your script has not declared variables named $chr, $m_start, $m_end, $d_start, and $d_end. You must declare them and assign values to them. See an example of this error and its remedy. If you don't assign values to them you will get a different error message saying values for those variables are undefined so you can't use them for concatenation in the following statement: print "$chr\t$m_start\t$m_end\t$d_start\t$d_end\n";

Hello,
I would like to map columns chr, start, end for dbSNP with chr, start, end for mirna and extract common lines with same chr, start, end positions. I have written a perl script where I found an error while running. could you please check it out and send me. I would be glad for your help.

Regards,
Rocky

#!/usr/bin/perl -w

use strict;
use warnings;
use DBI;

my $user = 'root';
my $password = '1004';

# connect to the database
my $dbh = DBI->connect("dbi:mysql:mirvar", $user, $password) || die "Failed connect DB : $!\n";

#my $sql;

#$sql = "select d.chr, m.Start as m_start, m.End as m_end, d.Start as d_start, d.End as d_end from mirna as m, dbsnp as d limit 100";
#my $sql1 = "select * from mirna limit 100";
my $sql1 = "select * from mirna limit 100";
my $sql2 = "select * from dbsnp limit 100";

#my $sth = $dbh->prepare($sql);
my $sth1 = $dbh->prepare($sql1);
my $sth2 = $dbh->prepare($sql2);

#$sth->execute || die "Error! : $sql\n";
$sth1->execute || die "Error! : $sql1\n";
$sth2->execute || die "Error! : $sql2\n";

#while ( my $line1 = $sth1->fetchrow_hashref() ) {
#       while ( my $line2 = $sth2->fetchrow_hashref() ) {
#               if ( $line2->{'Start'} <= $line1->{'Start'} && $line1->{'End'} <= $line2->{'End'} ) {
#                       print "test";
#               }
#       }
#}


while( my $dbsnp = $sth1->fetchrow_hashref() ){

  my $dbsnp_chr = $dbsnp->{'chr'};
  my $dbsnp_start = $dbsnp->{'d_start'};
  my $dbsnp_end = $dbsnp->{'d_end'};
   
while( my $mirna = $sth2->fetchrow_hashref() ){

  my $mirna_chr = $mirna->{'chr'};
  my $mirna_start = $mirna->{'Start'};
  my $mirna_end = $mirna->{'End'};

# to do~ comparison code~

  if($dbsnp_chr eq $mirna_chr && $dbsnp_start == $mirna_start || $dbsnp_end == $mirna_end || ($dbsnp_start >= $mirna_start && $dbsnp_end >= $mirna_end))
print "$dbsnp_chr\t$dbsnp_start\t$dbsnp_end\t$mirna_chr\t$mirna_start\t$mirna_end\n";
}
}

OUTPUT

[haojamrocky@melon hg18]$ perl test5.pl
syntax error at test5.pl line 52, near ")
print"
Execution of test5.pl aborted due to compilation errors.

Attachments
+------+-----------+-----------+------------+-------------+--------+
| chr  | Start     | End       | rsID       | orientation | strand |
+------+-----------+-----------+------------+-------------+--------+
| chr1 |   6946796 |   6946821 | rs57898978 | 0           | +      | 
| chr1 |   8912885 |   8912910 | rs57188530 | 0           | +      | 
| chr1 |  34340790 |  34340885 | rs6143185  | 0           | +      | 
| chr1 | 102891517 | 102891542 | rs56752146 | 0           | +      | 
| chr1 | 116916223 | 116916227 | rs3833909  | 0           | -      | 
| chr1 | 172228602 | 172228627 | rs56731360 | 0           | +      | 
| chr1 | 206307328 | 206307328 | rs35720470 | 0           | +      | 
| chr1 | 223739903 | 223739928 | rs59122179 | 0           | +      | 
| chr1 |       433 |       433 | rs56289060 | 0           | +      | 
| chr1 |       491 |       492 | rs55998931 | 0           | +      | 
| chr1 |       518 |       519 | rs62636508 | 0           | +      | 
| chr1 |       582 |       583 | rs58108140 | 0           | +      | 
| chr1 |       690 |       691 | rs10218492 | 0           | +      | 
| chr1 |       766 |       767 | rs10218493 | 0           | +      | 
| chr1 |       789 |       790 | rs10218527 | 0           | +      | 
| chr1 |       800 |       801 | rs28853987 | 0           | +      | 
| chr1 |       876 |       877 | rs28484712 | 0           | +      | 
| chr1 |       884 |       885 | rs28775022 | 0           | +      | 
| chr1 |       884 |       885 | rs62636509 | 0           | +      | 
| chr1 |       943 |       944 | rs10218495 | 0           | +      | 
| chr1 |      1016 |      1017 | rs62635278 | 0           | +      | 
| chr1 |      1029 |      1030 | rs62635279 | 0           | +      | 
| chr1 |      1271 |      1272 | rs9803797  | 0           | +      | 
| chr1 |      1319 |      1320 | rs2758124  | 0           | -      | 
| chr1 |      1332 |      1333 | rs3950659  | 0           | -      | 
| chr1 |      1370 |      1371 | rs3877545  | 0           | -      | 
| chr1 |      1404 |      1405 | rs2758123  | 0           | -      | 
| chr1 |      1427 |      1428 | rs2691333  | 0           | -      | 
| chr1 |      1468 |      1469 | rs62162368 | 0           | -      | 
| chr1 |      1539 |      1540 | rs4030196  | 0           | -      | 
| chr1 |      1554 |      1555 | rs2363296  | 0           | -      | 
| chr1 |      1591 |      1592 | rs4592209  | 0           | +      | 
| chr1 |      1643 |      1644 | rs61427470 | 0           | -      | 
| chr1 |      1643 |      1644 | rs62162367 | 0           | -      | 
| chr1 |      1649 |      1650 | rs57905273 | 0           | -      | 
| chr1 |      1665 |      1666 | rs62162366 | 0           | -      | 
| chr1 |      1730 |      1731 | rs11510383 | 0           | -      | 
| chr1 |      1757 |      1758 | rs4030194  | 0           | -      | 
| chr1 |      1783 |      1784 | rs57442816 | 0           | -      | 
| chr1 |      1808 |      1809 | rs4849250  | 0           | -      | 
| chr1 |      1809 |      1810 | rs7564627  | 0           | -      | 
| chr1 |      1823 |      1824 | rs2981848  | 0           | -      | 
| chr1 |      1825 |      1826 | rs2462500  | 0           | -      | 
| chr1 |      1832 |      1833 | rs7357973  | 0           | -      | 
| chr1 |      1863 |      1864 | rs62028714 | 0           | +      | 
| chr1 |      1911 |      1912 | rs7357889  | 0           | -      | 
| chr1 |      1936 |      1937 | rs11510263 | 0           | -      | 
| chr1 |      1936 |      1937 | rs62162365 | 0           | -      | 
| chr1 |      1983 |      1984 | rs7357887  | 0           | -      | 
| chr1 |      2032 |      2033 | rs2974776  | 0           | +      | 
| chr1 |      2060 |      2061 | rs3871692  | 0           | -      | 
| chr1 |      2060 |      2061 | rs62635282 | 0           | +      | 
| chr1 |      2065 |      2066 | rs3871693  | 0           | -      | 
| chr1 |      2076 |      2077 | rs2441649  | 0           | -      | 
| chr1 |      2090 |      2091 | rs7340201  | 0           | -      | 
| chr1 |      2106 |      2107 | rs11897134 | 0           | -      | 
| chr1 |      2127 |      2128 | rs2475482  | 0           | -      | 
| chr1 |      2154 |      2155 | rs7340200  | 0           | -      | 
| chr1 |      2168 |      2169 | rs2981847  | 0           | -      | 
| chr1 |      2195 |      2196 | rs2981846  | 0           | -      | 
| chr1 |      2245 |      2246 | rs62635283 | 0           | +      | 
| chr1 |      2289 |      2290 | rs28491605 | 0           | +      | 
| chr1 |      2295 |      2296 | rs2475481  | 0           | -      | 
| chr1 |      2342 |      2343 | rs62028715 | 0           | +      | 
| chr1 |      2351 |      2352 | rs62028716 | 0           | +      | 
| chr1 |      2368 |      2369 | rs2441647  | 0           | -      | 
| chr1 |      2379 |      2380 | rs3950657  | 0           | -      | 
| chr1 |      2395 |      2396 | rs62028717 | 0           | +      | 
| chr1 |      2469 |      2470 | rs2974781  | 0           | +      | 
| chr1 |      2634 |      2635 | rs11510117 | 0           | +      | 
| chr1 |      2636 |      2637 | rs11510118 | 0           | +      | 
| chr1 |      2642 |      2643 | rs2949418  | 0           | +      | 
| chr1 |      2645 |      2646 | rs62635284 | 0           | +      | 
| chr1 |      2655 |      2656 | rs11510119 | 0           | +      | 
| chr1 |      2669 |      2670 | rs62635285 | 0           | +      | 
| chr1 |      2810 |      2811 | rs2462499  | 0           | -      | 
| chr1 |      2886 |      2887 | rs2462498  | 0           | -      | 
| chr1 |      2978 |      2979 | rs62635286 | 0           | +      | 
| chr1 |      2980 |      2981 | rs62028691 | 0           | -      | 
| chr1 |      3000 |      3001 | rs12239753 | 0           | +      | 
| chr1 |      3016 |      3017 | rs2691331  | 0           | -      | 
| chr1 |      3020 |      3021 | rs12239425 | 0           | +      | 
| chr1 |      3022 |      3023 | rs12239277 | 0           | +      | 
| chr1 |      3040 |      3041 | rs62028689 | 0           | -      | 
| chr1 |      3164 |      3165 | rs2691330  | 0           | -      | 
| chr1 |      3164 |      3165 | rs28434453 | 0           | -      | 
| chr1 |      3164 |      3165 | rs28532600 | 0           | -      | 
| chr1 |      3189 |      3190 | rs2691329  | 0           | -      | 
| chr1 |      3223 |      3224 | rs4951865  | 0           | +      | 
| chr1 |      3262 |      3263 | rs4951866  | 0           | +      | 
| chr1 |      3286 |      3287 | rs4951867  | 0           | +      | 
| chr1 |      3321 |      3322 | rs2747970  | 0           | -      | 
| chr1 |      3335 |      3336 | rs2592733  | 0           | -      | 
| chr1 |      3354 |      3355 | rs28455646 | 0           | -      | 
| chr1 |      3370 |      3371 | rs28461966 | 0           | -      | 
| chr1 |      3370 |      3371 | rs4951868  | 0           | +      | 
| chr1 |      3419 |      3420 | rs2981841  | 0           | -      | 
| chr1 |      3475 |      3476 | rs4951869  | 0           | +      | 
| chr1 |      3526 |      3527 | rs2974786  | 0           | +      | 
| chr1 |      3529 |      3530 | rs7536480  | 0           | +      |
+--------+-----------+-----------+--------+------------------+------------------------+
| chr    | Start     | End       | strand | ACC              | ID                     |
+--------+-----------+-----------+--------+------------------+------------------------+
| chr 1  |     20229 |     20366 | +      | ACC="MI0006363"; | ID="hsa-mir-1302-2";   | 
| chr 1  |    556050 |    556128 | -      | ACC="MI0009987"; | ID="hsa-mir-1977";     | 
| chr 1  |   1092347 |   1092441 | +      | ACC="MI0000342"; | ID="hsa-mir-200b";     | 
| chr 1  |   1093106 |   1093195 | +      | ACC="MI0000737"; | ID="hsa-mir-200a";     | 
| chr 1  |   1094248 |   1094330 | +      | ACC="MI0001641"; | ID="hsa-mir-429";      | 
| chr 1  |   3467119 |   3467214 | -      | ACC="MI0003556"; | ID="hsa-mir-551a";     | 
| chr 1  |   9134314 |   9134423 | -      | ACC="MI0000268"; | ID="hsa-mir-34a";      | 
| chr 1  |  19096152 |  19096229 | -      | ACC="MI0006352"; | ID="hsa-mir-1290";     | 
| chr 1  |  21187394 |  21187512 | -      | ACC="MI0006390"; | ID="hsa-mir-1256";     | 
| chr 1  |  26753620 |  26753671 | +      | ACC="MI0009986"; | ID="hsa-mir-1976";     | 
| chr 1  |  34907787 |  34907882 | -      | ACC="MI0003557"; | ID="hsa-mir-552";      | 
| chr 1  |  40992614 |  40992705 | +      | ACC="MI0000749"; | ID="hsa-mir-30e";      | 
| chr 1  |  40995543 |  40995631 | +      | ACC="MI0000736"; | ID="hsa-mir-30c-1";    | 
| chr 1  |  65296705 |  65296779 | -      | ACC="MI0000103"; | ID="hsa-mir-101-1";    | 
| chr 1  |  68421789 |  68421881 | -      | ACC="MI0006397"; | ID="hsa-mir-1262";     | 
| chr 1  |  71305902 |  71305987 | -      | ACC="MI0000483"; | ID="hsa-mir-186";      | 
| chr 1  |  94084976 |  94085055 | +      | ACC="MI0005567"; | ID="hsa-mir-760";      | 
| chr 1  |  98284214 |  98284315 | -      | ACC="MI0000454"; | ID="hsa-mir-137";      | 
| chr 1  | 100519385 | 100519452 | +      | ACC="MI0003558"; | ID="hsa-mir-553";      | 
| chr 1  | 109943038 | 109943112 | +      | ACC="MI0000239"; | ID="hsa-mir-197";      | 
| chr 1  | 117015894 | 117015972 | +      | ACC="MI0003776"; | ID="hsa-mir-320b-1";   | 
| chr 1  | 117438788 | 117438873 | +      | ACC="MI0005767"; | ID="hsa-mir-942";      | 
| chr 1  | 149784896 | 149784991 | +      | ACC="MI0003559"; | ID="hsa-mir-554";      | 
| chr 1  | 152432765 | 152432843 | -      | ACC="MI0005545"; | ID="hsa-mir-190b";     | 
| chr 1  | 153431592 | 153431687 | +      | ACC="MI0003560"; | ID="hsa-mir-92b";      | 
| chr 1  | 153582765 | 153582860 | -      | ACC="MI0003561"; | ID="hsa-mir-555";      | 
| chr 1  | 154656757 | 154656845 | -      | ACC="MI0000466"; | ID="hsa-mir-9-1";      | 
| chr 1  | 155172547 | 155172660 | -      | ACC="MI0005116"; | ID="hsa-mir-765";      | 
| chr 1  | 160578960 | 160579054 | +      | ACC="MI0003562"; | ID="hsa-mir-556";      | 
| chr 1  | 164390604 | 164390659 | -      | ACC="MI0005713"; | ID="hsa-mir-921";      | 
| chr 1  | 166234522 | 166234588 | +      | ACC="MI0006436"; | ID="hsa-mir-1255b-2";  | 
| chr 1  | 166611386 | 166611483 | +      | ACC="MI0003563"; | ID="hsa-mir-557";      | 
| chr 1  | 169337493 | 169337571 | -      | ACC="MI0006357"; | ID="hsa-mir-1295";     | 
| chr 1  | 170374561 | 170374670 | -      | ACC="MI0000290"; | ID="hsa-mir-214";      | 
| chr 1  | 170380298 | 170380407 | -      | ACC="MI0000281"; | ID="hsa-mir-199a-2";   | 
| chr 1  | 175265122 | 175265204 | -      | ACC="MI0003123"; | ID="hsa-mir-488";      | 
| chr 1  | 191372256 | 191372336 | +      | ACC="MI0006425"; | ID="hsa-mir-1278";     | 
| chr 1  | 197094625 | 197094734 | -      | ACC="MI0000270"; | ID="hsa-mir-181b-1";   | 
| chr 1  | 197094796 | 197094905 | -      | ACC="MI0000289"; | ID="hsa-mir-181a-1";   | 
| chr 1  | 200044362 | 200044453 | +      | ACC="MI0006321"; | ID="hsa-mir-1231";     | 
| chr 1  | 203684053 | 203684149 | -      | ACC="MI0000810"; | ID="hsa-mir-135b";     | 
| chr 1  | 206041820 | 206041907 | -      | ACC="MI0000735"; | ID="hsa-mir-29c";      | 
| chr 1  | 206042411 | 206042491 | -      | ACC="MI0000107"; | ID="hsa-mir-29b-2";    | 
| chr 1  | 207672101 | 207672210 | +      | ACC="MI0000285"; | ID="hsa-mir-205";      | 
| chr 1  | 218357818 | 218357927 | -      | ACC="MI0000291"; | ID="hsa-mir-215";      | 
| chr 1  | 218358122 | 218358206 | -      | ACC="MI0000488"; | ID="hsa-mir-194-1";    | 
| chr 1  | 218440503 | 218440584 | -      | ACC="MI0006442"; | ID="hsa-mir-664";      | 
| chr 1  | 222511329 | 222511466 | -      | ACC="MI0003839"; | ID="hsa-mir-320b-2";   | 
| chr 1  | 229222197 | 229222293 | -      | ACC="MI0006275"; | ID="hsa-mir-1182";     | 
| chr 1  | 234082923 | 234082983 | -      | ACC="MI0007258"; | ID="hsa-mir-1537";     | 
| chr 2  |  25405013 |  25405094 | -      | ACC="MI0003815"; | ID="hsa-mir-1301";     | 
| chr 2  |  32610724 |  32610817 | +      | ACC="MI0003564"; | ID="hsa-mir-558";      | 
| chr 2  |  47458318 |  47458413 | +      | ACC="MI0003565"; | ID="hsa-mir-559";      | 
| chr 2  |  56063606 |  56063715 | -      | ACC="MI0000293"; | ID="hsa-mir-217";      | 
| chr 2  |  56069589 |  56069698 | -      | ACC="MI0000292"; | ID="hsa-mir-216a";     | 
| chr 2  |  56081353 |  56081434 | -      | ACC="MI0005569"; | ID="hsa-mir-216b";     | 
| chr 2  |  70333554 |  70333641 | -      | ACC="MI0006347"; | ID="hsa-mir-1285-2";   | 
| chr 2  | 114057006 | 114057143 | -      | ACC="MI0006364"; | ID="hsa-mir-1302-3";   | 
| chr 2  | 132731009 | 132731123 | -      | ACC="MI0006336"; | ID="hsa-mir-663b";     | 
| chr 2  | 136139437 | 136139518 | +      | ACC="MI0000447"; | ID="hsa-mir-128-1";    | 
| chr 2  | 149355835 | 149355887 | -      | ACC="MI0009988"; | ID="hsa-mir-1978";     | 
| chr 2  | 175740607 | 175740683 | -      | ACC="MI0005755"; | ID="hsa-mir-933";      | 
| chr 2  | 176723277 | 176723386 | +      | ACC="MI0000267"; | ID="hsa-mir-10b";      | 
| chr 2  | 177173954 | 177174026 | -      | ACC="MI0006381"; | ID="hsa-mir-1246";     | 
| chr 2  | 180433808 | 180433880 | -      | ACC="MI0006392"; | ID="hsa-mir-1258";     | 
| chr 2  | 188870464 | 188870560 | +      | ACC="MI0003567"; | ID="hsa-mir-561";      | 
| chr 2  | 189551063 | 189551132 | +      | ACC="MI0006380"; | ID="hsa-mir-1245";     | 
| chr 2  | 207842244 | 207842393 | -      | ACC="MI0006365"; | ID="hsa-mir-1302-4";   | 
| chr 2  | 212999232 | 212999329 | -      | ACC="MI0006375"; | ID="hsa-mir-548f-2";   | 
| chr 2  | 218975613 | 218975689 | +      | ACC="MI0000084"; | ID="hsa-mir-26b";      | 
| chr 2  | 219574611 | 219574674 | -      | ACC="MI0000783"; | ID="hsa-mir-375";      | 
| chr 2  | 219867077 | 219867166 | -      | ACC="MI0000463"; | ID="hsa-mir-153-1";    | 
| chr 2  | 232286268 | 232286352 | +      | ACC="MI0006379"; | ID="hsa-mir-1244";     | 
| chr 2  | 232465196 | 232465252 | -      | ACC="MI0007076"; | ID="hsa-mir-1471";     | 
| chr 2  | 232745607 | 232745701 | +      | ACC="MI0003568"; | ID="hsa-mir-562";      | 
| chr 2  | 241044091 | 241044179 | +      | ACC="MI0000478"; | ID="hsa-mir-149";      | 
| chr 3  |  10411173 |  10411246 | -      | ACC="MI0005560"; | ID="hsa-mir-885";      | 
| chr 3  |  15890282 |  15890360 | +      | ACC="MI0003569"; | ID="hsa-mir-563";      | 
| chr 3  |  35760972 |  35761055 | +      | ACC="MI0000727"; | ID="hsa-mir-128-2";    | 
| chr 3  |  37985899 |  37985975 | +      | ACC="MI0000083"; | ID="hsa-mir-26a-1";    | 
| chr 3  |  44130708 |  44130806 | +      | ACC="MI0000476"; | ID="hsa-mir-138-1";    | 
| chr 3  |  44878384 |  44878477 | +      | ACC="MI0003570"; | ID="hsa-mir-564";      | 
| chr 3  |  47866049 |  47866123 | +      | ACC="MI0006313"; | ID="hsa-mir-1226";     | 
| chr 3  |  49032585 |  49032671 | -      | ACC="MI0001448"; | ID="hsa-mir-425";      | 
| chr 3  |  49033055 |  49033146 | -      | ACC="MI0000465"; | ID="hsa-mir-191";      | 
| chr 3  |  50185763 |  50185856 | +      | ACC="MI0003572"; | ID="hsa-mir-566";      | 
| chr 3  |  52277334 |  52277417 | -      | ACC="MI0000433"; | ID="hsa-let-7g";       | 
| chr 3  |  52303275 |  52303364 | -      | ACC="MI0000452"; | ID="hsa-mir-135a-1";   | 
| chr 3  |  71673811 |  71673930 | -      | ACC="MI0006431"; | ID="hsa-mir-1284";     | 
| chr 3  |  75762604 |  75762699 | +      | ACC="MI0006657"; | ID="hsa-mir-1324";     | 
| chr 3  | 113314338 | 113314435 | +      | ACC="MI0003573"; | ID="hsa-mir-567";      | 
| chr 3  | 115518012 | 115518106 | -      | ACC="MI0003574"; | ID="hsa-mir-568";      | 
| chr 3  | 121597205 | 121597266 | -      | ACC="MI0000240"; | ID="hsa-mir-198";      | 
| chr 3  | 126991937 | 126992085 | -      | ACC="MI0006421"; | ID="hsa-mir-548i-1";   | 
| chr 3  | 129563698 | 129563791 | +      | ACC="MI0006437"; | ID="hsa-mir-1280";     | 
| chr 3  | 161605070 | 161605167 | +      | ACC="MI0000438"; | ID="hsa-mir-15b";      | 
| chr 3  | 161605227 | 161605307 | +      | ACC="MI0000115"; | ID="hsa-mir-16-2";     | 
| chr 3  | 165371953 | 165372038 | -      | ACC="MI0006398"; | ID="hsa-mir-1263";     | 
| chr 3  | 165541823 | 165541932 | +      | ACC="MI0006654"; | ID="hsa-mir-720";      | 
| chr 3  | 169752336 | 169752431 | +      | ACC="MI0003575"; | ID="hsa-mir-551b";     | 
| chr 3  | 172307147 | 172307242 | -      | ACC="MI0003576"; | ID="hsa-mir-569";      | 
| chr 3  | 185441887 | 185441971 | +      | ACC="MI0003764"; | ID="hsa-mir-1224";     | 
| chr 3  | 187987155 | 187987260 | +      | ACC="MI0006383"; | ID="hsa-mir-1248";     | 
| chr 3  | 189889263 | 189889348 | +      | ACC="MI0000086"; | ID="hsa-mir-28";       | 
| chr 3  | 191030405 | 191030492 | +      | ACC="MI0005769"; | ID="hsa-mir-944";      | 
| chr 3  | 196911452 | 196911548 | +      | ACC="MI0003577"; | ID="hsa-mir-570";      | 
| chr 3  | 198885764 | 198885844 | -      | ACC="MI0005714"; | ID="hsa-mir-922";      | 
| chr 4  |    333946 |    334041 | +      | ACC="MI0003578"; | ID="hsa-mir-571";      | 
| chr 4  |   1957909 |   1958002 | -      | ACC="MI0005768"; | ID="hsa-mir-943";      | 
| chr 4  |   8057928 |   8058008 | -      | ACC="MI0000097"; | ID="hsa-mir-95";       | 
| chr 4  |   9166887 |   9167035 | -      | ACC="MI0006422"; | ID="hsa-mi

Hello,
I would like to map columns chr, start, end for dbSNP with chr, start, end for mirna and extract common lines with same chr, start, end positions and also considering within the start and end positions too. I have written a perl script where I found an error while running. could you please check it out and send me. I would be glad for your help.

Regards,
Rocky

Dear Sir,

I would like to map values in columns and extract attributes with same values as below.

CONDITION:-
same chrID in dbsnp129 with mirna text files
same chromStart and chromEnd or within these two positions.

I hereby attached the two tables in mysql.

Regards,
Rocky

#!/usr/bin/perl -w
use warnings;
###Perl Script to map SNPs in microRNAs####
###USAGE: Map_miRNA_SNP.pl <input miRNA file> <input SNP file> <output file>###


#if (scalar @ARGV <3)
#       {
#               print "Check Usage of the program\n";
#       }
#$infile_mirna=$ARGV[0];
open (IN, "/home/haojamrocky/DATA/hg18/mirna/pre-mirna") or die;
while ($read = <IN>)
        {
                chomp $read;
                $read =~ s/\r//g;
                @datarr = split '\t', $read;

                push @Chr, $datarr[0];
                push @Chrstart, $datarr[1];
                push @Chrend, $datarr[2];
                push @Chrstrand, $datarr[3];
                push @Chr_mirna, $datarr[4];
        }
                #$infile_SNP="$ARGV[1]";
                open (SNP, "/home/haojamrocky/DATA/hg18/dbsnp/dbsnp129/dbsnp129.txt") or die print "Enter a valid file name on command line\n";
                #open WRITE, ">$ARGV[2]" or die;
                #print WRITE "Chr\tmiRNA\tStrand\tSNP\tSNPstrand\tmiRStart\tmiRStop\tSNP_POS\tAllele\trefNCBI\trefUCSC\tObserved\tValidation Status\n";

                while ($snp_each = <SNP>)
                        {
                                chomp $snp_each;
                                $snp_each=~ s/\r//g;
                                @snp_data = split("\t", $snp_each);
                                for ($i = 0; $i <= scalar@Chr; $i++)
                                        {
                                                                if ($Chr[$i] =~ /^$snp_data[1]$/ && $snp_data[3] >= $Chrstart[$i] && $snp_data[3] <=  $Chrend [$i] )
                                                        {
                                                                print WRITE "$Chr[$i]\t$Chr_mirna[$i]\t$Chrstrand[$i]\t$snp_data[4]\t$snp_data[6]\t$Chrstart[$i]\t$Chrend[$i]\t$snp_data[2]\t$snp_data[9]\t$snp_data[8]\t$snp_data[7]\t$snp_data[10]\t$snp_data[12]\n";
                                                        }
                                        }


                        }
Attachments
585	chr1	433	433	rs56289060	0	+	-	-	-/C	genomic	insertion	unknown	0	0	unknown	between	1
585	chr1	491	492	rs55998931	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	518	519	rs62636508	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	582	583	rs58108140	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	690	691	rs10218492	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	1
585	chr1	766	767	rs10218493	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	789	790	rs10218527	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	800	801	rs28853987	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	876	877	rs28484712	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	884	885	rs28775022	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	884	885	rs62636509	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	943	944	rs10218495	0	+	G	G	G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1016	1017	rs62635278	0	+	A	A	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1029	1030	rs62635279	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1271	1272	rs9803797	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1319	1320	rs2758124	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1332	1333	rs3950659	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1370	1371	rs3877545	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1404	1405	rs2758123	0	-	A	A	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1427	1428	rs2691333	0	-	G	G	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1468	1469	rs62162368	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1539	1540	rs4030196	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1554	1555	rs2363296	0	-	A	A	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1591	1592	rs4592209	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1643	1644	rs61427470	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1643	1644	rs62162367	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1649	1650	rs57905273	0	-	T	T	-/A	genomic	deletion	unknown	0	0	unknown	exact	3
585	chr1	1665	1666	rs62162366	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1730	1731	rs11510383	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1757	1758	rs4030194	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1783	1784	rs57442816	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1808	1809	rs4849250	0	-	C	C	A/G	genomic	single	by-2hit-2allele	0	0	unknown	exact	3
585	chr1	1809	1810	rs7564627	0	-	G	G	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1823	1824	rs2981848	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1825	1826	rs2462500	0	-	G	G	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1832	1833	rs7357973	0	-	A	A	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1863	1864	rs62028714	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1911	1912	rs7357889	0	-	C	C	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1936	1937	rs11510263	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1936	1937	rs62162365	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1983	1984	rs7357887	0	-	C	C	G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2032	2033	rs2974776	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2060	2061	rs3871692	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2060	2061	rs62635282	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2065	2066	rs3871693	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2076	2077	rs2441649	0	-	C	C	C/G	genomic	single	by-submitter	0	0	unknown	exact	3
585	chr1	2090	2091	rs7340201	0	-	G	G	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2106	2107	rs11897134	0	-	C	C	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2127	2128	rs2475482	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2154	2155	rs7340200	0	-	G	G	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2168	2169	rs2981847	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2195	2196	rs2981846	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2245	2246	rs62635283	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2289	2290	rs28491605	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2295	2296	rs2475481	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2342	2343	rs62028715	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2351	2352	rs62028716	0	+	G	G	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2368	2369	rs2441647	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2379	2380	rs3950657	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2395	2396	rs62028717	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2469	2470	rs2974781	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2634	2635	rs11510117	0	+	A	A	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2636	2637	rs11510118	0	+	G	G	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2642	2643	rs2949418	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2645	2646	rs62635284	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2655	2656	rs11510119	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2669	2670	rs62635285	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2810	2811	rs2462499	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2886	2887	rs2462498	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2978	2979	rs62635286	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2980	2981	rs62028691	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3000	3001	rs12239753	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3016	3017	rs2691331	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3020	3021	rs12239425	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3022	3023	rs12239277	0	+	A	A	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3040	3041	rs62028689	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3164	3165	rs2691330	0	-	C	C	A/C/G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3164	3165	rs28434453	0	-	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3164	3165	rs28532600	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3189	3190	rs2691329	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3223	3224	rs4951865	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3262	3263	rs4951866	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3286	3287	rs4951867	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3321	3322	rs2747970	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3335	3336	rs2592733	0	-	T	T	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3354	3355	rs28455646	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3370	3371	rs28461966	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3370	3371	rs4951868	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3419	3420	rs2981841	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3475	3476	rs4951869	0	+	T	T	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3526	3527	rs2974786	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3529	3530	rs7536480	0	+	C	C	C/T	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3530	3531	rs2691328	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3546	3547	rs4951870	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3591	3592	rs2691327	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3612	3613	rs2691326	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3638	3639	rs2691325	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3661	3662	rs7523129	0	+	T	T	G/T	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3675	3676	rs28719485	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3675	3676	rs7166048	0	-	T	T	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3691	3692	rs11490436	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3697	3698	rs11490238	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs28391190	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs28428499	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs7164031	0	-	C	C	A/G	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3767	3768	rs2974788	0	+	A	A	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3767	3768	rs62028756	0	+	A	A	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3774	3775	rs2691324	0	-	G	G	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3797	3798	rs62530143	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3797	3798	rs7536681	0	+	C	C	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3808	3809	rs62530144	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3808	3809	rs7544137	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3834	3835	rs62530145	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3834	3835	rs7536753	0	+	C	C	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3842	3843	rs2592732	0	-	T	T	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3842	3843	rs62635296	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3843	3844	rs5940665	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3844	3845	rs7163793	0	-	C	C	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3888	3889	rs2758121	0	-	T	T	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3924	3925	rs2974790	0	+	C	C	C/T	genomic	single	unknow
chr1 20229 20366 + ACC="MI0006363"; ID="hsa-mir-1302-2"; 
chr1 556050 556128 - ACC="MI0009987"; ID="hsa-mir-1977"; 
chr1 1092347 1092441 + ACC="MI0000342"; ID="hsa-mir-200b"; 
chr1 1093106 1093195 + ACC="MI0000737"; ID="hsa-mir-200a"; 
chr1 1094248 1094330 + ACC="MI0001641"; ID="hsa-mir-429"; 
chr1 3467119 3467214 - ACC="MI0003556"; ID="hsa-mir-551a"; 
chr1 9134314 9134423 - ACC="MI0000268"; ID="hsa-mir-34a"; 
chr1 19096152 19096229 - ACC="MI0006352"; ID="hsa-mir-1290"; 
chr1 21187394 21187512 - ACC="MI0006390"; ID="hsa-mir-1256"; 
chr1 26753620 26753671 + ACC="MI0009986"; ID="hsa-mir-1976"; 
chr1 34907787 34907882 - ACC="MI0003557"; ID="hsa-mir-552"; 
chr1 40992614 40992705 + ACC="MI0000749"; ID="hsa-mir-30e"; 
chr1 40995543 40995631 + ACC="MI0000736"; ID="hsa-mir-30c-1"; 
chr1 65296705 65296779 - ACC="MI0000103"; ID="hsa-mir-101-1"; 
chr1 68421789 68421881 - ACC="MI0006397"; ID="hsa-mir-1262"; 
chr1 71305902 71305987 - ACC="MI0000483"; ID="hsa-mir-186"; 
chr1 94084976 94085055 + ACC="MI0005567"; ID="hsa-mir-760"; 
chr1 98284214 98284315 - ACC="MI0000454"; ID="hsa-mir-137"; 
chr1 100519385 100519452 + ACC="MI0003558"; ID="hsa-mir-553"; 
chr1 109943038 109943112 + ACC="MI0000239"; ID="hsa-mir-197"; 
chr1 117015894 117015972 + ACC="MI0003776"; ID="hsa-mir-320b-1"; 
chr1 117438788 117438873 + ACC="MI0005767"; ID="hsa-mir-942"; 
chr1 149784896 149784991 + ACC="MI0003559"; ID="hsa-mir-554"; 
chr1 152432765 152432843 - ACC="MI0005545"; ID="hsa-mir-190b"; 
chr1 153431592 153431687 + ACC="MI0003560"; ID="hsa-mir-92b"; 
chr1 153582765 153582860 - ACC="MI0003561"; ID="hsa-mir-555"; 
chr1 154656757 154656845 - ACC="MI0000466"; ID="hsa-mir-9-1"; 
chr1 155172547 155172660 - ACC="MI0005116"; ID="hsa-mir-765"; 
chr1 160578960 160579054 + ACC="MI0003562"; ID="hsa-mir-556"; 
chr1 164390604 164390659 - ACC="MI0005713"; ID="hsa-mir-921"; 
chr1 166234522 166234588 + ACC="MI0006436"; ID="hsa-mir-1255b-2"; 
chr1 166611386 166611483 + ACC="MI0003563"; ID="hsa-mir-557"; 
chr1 169337493 169337571 - ACC="MI0006357"; ID="hsa-mir-1295"; 
chr1 170374561 170374670 - ACC="MI0000290"; ID="hsa-mir-214"; 
chr1 170380298 170380407 - ACC="MI0000281"; ID="hsa-mir-199a-2"; 
chr1 175265122 175265204 - ACC="MI0003123"; ID="hsa-mir-488"; 
chr1 191372256 191372336 + ACC="MI0006425"; ID="hsa-mir-1278"; 
chr1 197094625 197094734 - ACC="MI0000270"; ID="hsa-mir-181b-1"; 
chr1 197094796 197094905 - ACC="MI0000289"; ID="hsa-mir-181a-1"; 
chr1 200044362 200044453 + ACC="MI0006321"; ID="hsa-mir-1231"; 
chr1 203684053 203684149 - ACC="MI0000810"; ID="hsa-mir-135b"; 
chr1 206041820 206041907 - ACC="MI0000735"; ID="hsa-mir-29c"; 
chr1 206042411 206042491 - ACC="MI0000107"; ID="hsa-mir-29b-2"; 
chr1 207672101 207672210 + ACC="MI0000285"; ID="hsa-mir-205"; 
chr1 218357818 218357927 - ACC="MI0000291"; ID="hsa-mir-215"; 
chr1 218358122 218358206 - ACC="MI0000488"; ID="hsa-mir-194-1"; 
chr1 218440503 218440584 - ACC="MI0006442"; ID="hsa-mir-664"; 
chr1 222511329 222511466 - ACC="MI0003839"; ID="hsa-mir-320b-2"; 
chr1 229222197 229222293 - ACC="MI0006275"; ID="hsa-mir-1182"; 
chr1 234082923 234082983 - ACC="MI0007258"; ID="hsa-mir-1537"; 
chr2 25405013 25405094 - ACC="MI0003815"; ID="hsa-mir-1301"; 
chr2 32610724 32610817 + ACC="MI0003564"; ID="hsa-mir-558"; 
chr2 47458318 47458413 + ACC="MI0003565"; ID="hsa-mir-559"; 
chr2 56063606 56063715 - ACC="MI0000293"; ID="hsa-mir-217"; 
chr2 56069589 56069698 - ACC="MI0000292"; ID="hsa-mir-216a"; 
chr2 56081353 56081434 - ACC="MI0005569"; ID="hsa-mir-216b"; 
chr2 70333554 70333641 - ACC="MI0006347"; ID="hsa-mir-1285-2"; 
chr2 114057006 114057143 - ACC="MI0006364"; ID="hsa-mir-1302-3"; 
chr2 132731009 132731123 - ACC="MI0006336"; ID="hsa-mir-663b"; 
chr2 136139437 136139518 + ACC="MI0000447"; ID="hsa-mir-128-1"; 
chr2 149355835 149355887 - ACC="MI0009988"; ID="hsa-mir-1978"; 
chr2 175740607 175740683 - ACC="MI0005755"; ID="hsa-mir-933"; 
chr2 176723277 176723386 + ACC="MI0000267"; ID="hsa-mir-10b"; 
chr2 177173954 177174026 - ACC="MI0006381"; ID="hsa-mir-1246"; 
chr2 180433808 180433880 - ACC="MI0006392"; ID="hsa-mir-1258"; 
chr2 188870464 188870560 + ACC="MI0003567"; ID="hsa-mir-561"; 
chr2 189551063 189551132 + ACC="MI0006380"; ID="hsa-mir-1245"; 
chr2 207842244 207842393 - ACC="MI0006365"; ID="hsa-mir-1302-4"; 
chr2 212999232 212999329 - ACC="MI0006375"; ID="hsa-mir-548f-2"; 
chr2 218975613 218975689 + ACC="MI0000084"; ID="hsa-mir-26b"; 
chr2 219574611 219574674 - ACC="MI0000783"; ID="hsa-mir-375"; 
chr2 219867077 219867166 - ACC="MI0000463"; ID="hsa-mir-153-1"; 
chr2 232286268 232286352 + ACC="MI0006379"; ID="hsa-mir-1244"; 
chr2 232465196 232465252 - ACC="MI0007076"; ID="hsa-mir-1471"; 
chr2 232745607 232745701 + ACC="MI0003568"; ID="hsa-mir-562"; 
chr2 241044091 241044179 + ACC="MI0000478"; ID="hsa-mir-149"; 
chr3 10411173 10411246 - ACC="MI0005560"; ID="hsa-mir-885"; 
chr3 15890282 15890360 + ACC="MI0003569"; ID="hsa-mir-563"; 
chr3 35760972 35761055 + ACC="MI0000727"; ID="hsa-mir-128-2"; 
chr3 37985899 37985975 + ACC="MI0000083"; ID="hsa-mir-26a-1"; 
chr3 44130708 44130806 + ACC="MI0000476"; ID="hsa-mir-138-1"; 
chr3 44878384 44878477 + ACC="MI0003570"; ID="hsa-mir-564"; 
chr3 47866049 47866123 + ACC="MI0006313"; ID="hsa-mir-1226"; 
chr3 49032585 49032671 - ACC="MI0001448"; ID="hsa-mir-425"; 
chr3 49033055 49033146 - ACC="MI0000465"; ID="hsa-mir-191"; 
chr3 50185763 50185856 + ACC="MI0003572"; ID="hsa-mir-566"; 
chr3 52277334 52277417 - ACC="MI0000433"; ID="hsa-let-7g"; 
chr3 52303275 52303364 - ACC="MI0000452"; ID="hsa-mir-135a-1"; 
chr3 71673811 71673930 - ACC="MI0006431"; ID="hsa-mir-1284"; 
chr3 75762604 75762699 + ACC="MI0006657"; ID="hsa-mir-1324"; 
chr3 113314338 113314435 + ACC="MI0003573"; ID="hsa-mir-567"; 
chr3 115518012 115518106 - ACC="MI0003574"; ID="hsa-mir-568"; 
chr3 121597205 121597266 - ACC="MI0000240"; ID="hsa-mir-198"; 
chr3 126991937 126992085 - ACC="MI0006421"; ID="hsa-mir-548i-1"; 
chr3 129563698 129563791 + ACC="MI0006437"; ID="hsa-mir-1280"; 
chr3 161605070 161605167 + ACC="MI0000438"; ID="hsa-mir-15b"; 
chr3 161605227 161605307 + ACC="MI0000115"; ID="hsa-mir-16-2"; 
chr3 165371953 165372038 - ACC="MI0006398"; ID="hsa-mir-1263"; 
chr3 165541823 165541932 + ACC="MI0006654"; ID="hsa-mir-720"; 
chr3 169752336 169752431 + ACC="MI0003575"; ID="hsa-mir-551b"; 
chr3 172307147 172307242 - ACC="MI0003576"; ID="hsa-mir-569"; 
chr3 185441887 185441971 + ACC="MI0003764"; ID="hsa-mir-1224"; 
chr3 187987155 187987260 + ACC="MI0006383"; ID="hsa-mir-1248"; 
chr3 189889263 189889348 + ACC="MI0000086"; ID="hsa-mir-28"; 
chr3 191030405 191030492 + ACC="MI0005769"; ID="hsa-mir-944"; 
chr3 196911452 196911548 + ACC="MI0003577"; ID="hsa-mir-570"; 
chr3 198885764 198885844 - ACC="MI0005714"; ID="hsa-mir-922"; 
chr4 333946 334041 + ACC="MI0003578"; ID="hsa-mir-571"; 
chr4 1957909 1958002 - ACC="MI0005768"; ID="hsa-mir-943"; 
chr4 8057928 8058008 - ACC="MI0000097"; ID="hsa-mir-95"; 
chr4 9166887 9167035 - ACC="MI0006422"; ID="hsa-mir-548i-2"; 
chr4 10979549 10979643 + ACC="MI0003579"; ID="hsa-mir-572"; 
chr4 20138996 20139105 + ACC="MI0000294"; ID="hsa-mir-218-1"; 
chr4 24130913 24131011 - ACC="MI0003580"; ID="hsa-mir-573"; 
chr4 36104383 36104445 - ACC="MI0006435"; ID="hsa-mir-1255b-1"; 
chr4 38546048 38546143 + ACC="MI0003581"; ID="hsa-mir-574"; 
chr4 66825137 66825241 + ACC="MI0006406"; ID="hsa-mir-1269"; 
chr4 83893514 83893607 - ACC="MI0003582"; ID="hsa-mir-575"; 
chr4 102470482 102470594 - ACC="MI0006389"; ID="hsa-mir-1255a"; 
chr4 110629303 110629400 + ACC="MI0003583"; ID="hsa-mir-576"; 
chr4 112001187 112001252 - ACC="MI0005775"; ID="hsa-mir-297"; 
chr4 113788479 113788546 - ACC="MI0000775"; ID="hsa-mir-367"; 
chr4 113788609 113788676 - ACC="MI0000774"; ID="hsa-mir-302d"; 
chr4 113788788 113788856 - ACC="MI0000738"; ID="hsa-mir-302a"; 
chr4 113788968 113789035 - ACC="MI0000773"; ID="hsa-mir-302c"; 
chr4 113789090 113789162 - ACC="MI0000772"; ID="hsa-mir-302b"; 
chr4 114247468 114247560 + ACC="MI0006373"; ID="hsa-mir-1243"; 
chr4 115797364 115797459 + ACC="MI0003584"; ID="hsa-mir-577"; 
chr4 117440330 117440373 + ACC="MI0009983"; ID="hsa-mir-1973"; 
chr4 126647864 126647912 + ACC="MI0010488"; ID="hsa-mir-2054"; 
chr4 148485231 148485319 - ACC="MI0006395"; ID="hsa-mir-548g"; 
chr4 166526844 166526939 + ACC="MI0003585"; ID="hsa-mir-578"; 
chr4 166541264 166541339 - ACC="MI0009989"; ID="hsa-mir-1979"; 
chr4 183327440 183327525 + ACC="MI0006372"; ID="hsa-mir-1305"; 
chr5 15988291 15988369 + ACC="MI0005562"; ID="hsa-mir-887"; 
chr5 32430241 32430338 - ACC="MI0003586"; ID="hsa-mir-579"; 
chr5 36183751 36183847 - ACC="MI0003587"; ID="hsa-mir-580"; 
chr5 41511491 41511561 + ACC="MI0006410"; ID="hsa-mir-1274a"; 
chr5 53283091 53283186 - ACC="MI0003588"; ID="hsa-mir-581"; 
chr5 54502117 54502207 - ACC="MI0001648"; ID="hsa-mir-449a"; 
chr5 54502231 54502327 - ACC="MI0003673"; ID="hsa-mir-449b"; 
chr5 59035189 59035286 - ACC="MI0003589"; ID="hsa-mir-582"; 
chr5 87998427 87998513 - ACC="MI0000467"; ID="hsa-mir-9-2"; 
chr5 93930928 93930997 - ACC="MI0009984"; ID="hsa-mir-1974"; 
chr5 95440598 95440672 + ACC="MI0003590"; ID="hsa-mir-583"; 
chr5 100180085 100180168 - ACC="MI0006420"; ID="hsa-mir-548p"; 
chr5 109877429 109877515 - ACC="MI0006376"; ID="hsa-mir-548f-3"; 
chr5 118338180 118338264 + ACC="MI0006379"; ID="hsa-mir-1244"; 
chr5 132791187 132791297 - ACC="MI0006351"; ID="hsa-mir-1289-2"; 
chr5 135444076 135444196 - ACC="MI0005527"; ID="hsa-mir-886"; 
chr5 137011160 137011237 - ACC="MI0005532"; ID="hsa-mir-874"; 
chr5 148422069 148422165 - ACC="MI0003591"; ID="hsa-mir-584"; 
chr5 148788674 148788779 + ACC="MI0000459"; ID="hsa-mir-143"; 
chr5 148790402 148790489 + ACC="MI0000461"; ID="hsa-mir-145"; 
chr5 149092581 149092646 + ACC="MI0000786"; ID="hsa-mir-378"; 
chr5 153706859 153707000 + ACC="MI0006356"; ID="hsa-mir-1294"; 
chr5 154045529 154045614 + ACC="MI0006370"; ID="hsa-mir-1303"; 
chr5 159844937 159845035 + ACC="MI0000477"; ID="hsa-mir-146a"; 
chr5 167920479 167920556 - ACC="MI0000109"; ID="hsa-mir-103-1"; 
chr5 167920487 167920548 + ACC="MI0007261"; ID="hsa-mir-103-1-as"; 
chr5 168127729 168127838 - ACC="MI0000295"; ID="hsa-mir-218-2"; 
chr5 168623183 168623276 - ACC="MI0003592"; ID="hsa-mir-585"; 
chr5 175727555 175727640 + ACC="MI0003814"; ID="hs

Mr/ Mrs,
I am running a perl script for mapping the genomic positions i.e. the start and end positions to retrieve positions within the start and end. The script runs correctly in smaller text files, but it was running slowly for almost 4 days, how it could be run faster by rectifying the script attach here. The size for snp129.txt is 1.60 GB and TARGETSCAN is 2.20 MB I would be glad for your kindness. Hoping to recieve response soon.

Regards,
Rocky
SNU, College of Medicine
Seoul

#!/usr/bin/perl -w
#use strict;


open(IN, "/home/haojamrocky/snp129.txt") or die print "Enter a valid file name on command line\n";
@snp = <IN>; ## assigning snp 
close IN;

open(IN2, "/home/haojamrocky/DATA/hg18/miRTarget/TARGETSCAN") or die print "Cannot open mirna file\n";
@PITA = <IN2>; ## assigning mirna
close IN2;

for ($i=0; $i <= $#snp; $i++){
###################### SNP############################
        #$geneName = (split(/\t/,$refFlat[$i]))[0];
        #$name = (split(/\t/,$refFlat[$i]))[1];
        $chrom1 = (split(/\t/,$snp[$i]))[1];
        $chromStart1 = ((plit(/\t/,$sn)[$i]))[2];
        $chromEnd1 = (split(/\t/,$snp[$i]))[3];
########################(############)################
        foreach my $line(@PITA){     )
###################### m(rna #)#######################
                $chrom2 = (split(/\t/,$line))[0];
                $chromStart2 = (split(/\t/,$line))[1];
                $chromEnd2 = (split(/\t/,$line))[2];
#######################################################
        #            print "$chrom1 $chrom2\n";

                        if( $chrom1 eq $chrom2 && ( $chromStart1 >= $chromStart2 && $chromEnd1 <= $chromEnd2 )){
                        chomp $snp[$i]; chomp $line;
                        print "$snp[$i] \t $line \n";
                        }
                }
        }
print "\n";
exit;
Attachments
585	chr1	433	433	rs56289060	0	+	-	-	-/C	genomic	insertion	unknown	0	0	unknown	between	1
585	chr1	491	492	rs55998931	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	518	519	rs62636508	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	582	583	rs58108140	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	1
585	chr1	690	691	rs10218492	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	1
585	chr1	766	767	rs10218493	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	789	790	rs10218527	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	800	801	rs28853987	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	876	877	rs28484712	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	884	885	rs28775022	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	884	885	rs62636509	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	943	944	rs10218495	0	+	G	G	G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1016	1017	rs62635278	0	+	A	A	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1029	1030	rs62635279	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1271	1272	rs9803797	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1319	1320	rs2758124	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1332	1333	rs3950659	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1370	1371	rs3877545	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1404	1405	rs2758123	0	-	A	A	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1427	1428	rs2691333	0	-	G	G	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1468	1469	rs62162368	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1539	1540	rs4030196	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1554	1555	rs2363296	0	-	A	A	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1591	1592	rs4592209	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1643	1644	rs61427470	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1643	1644	rs62162367	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1649	1650	rs57905273	0	-	T	T	-/A	genomic	deletion	unknown	0	0	unknown	exact	3
585	chr1	1665	1666	rs62162366	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1730	1731	rs11510383	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1757	1758	rs4030194	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1783	1784	rs57442816	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1808	1809	rs4849250	0	-	C	C	A/G	genomic	single	by-2hit-2allele	0	0	unknown	exact	3
585	chr1	1809	1810	rs7564627	0	-	G	G	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1823	1824	rs2981848	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1825	1826	rs2462500	0	-	G	G	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1832	1833	rs7357973	0	-	A	A	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1863	1864	rs62028714	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1911	1912	rs7357889	0	-	C	C	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	1936	1937	rs11510263	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1936	1937	rs62162365	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	1983	1984	rs7357887	0	-	C	C	G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2032	2033	rs2974776	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2060	2061	rs3871692	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2060	2061	rs62635282	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2065	2066	rs3871693	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2076	2077	rs2441649	0	-	C	C	C/G	genomic	single	by-submitter	0	0	unknown	exact	3
585	chr1	2090	2091	rs7340201	0	-	G	G	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2106	2107	rs11897134	0	-	C	C	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2127	2128	rs2475482	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2154	2155	rs7340200	0	-	G	G	C/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	2168	2169	rs2981847	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2195	2196	rs2981846	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2245	2246	rs62635283	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2289	2290	rs28491605	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2295	2296	rs2475481	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2342	2343	rs62028715	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2351	2352	rs62028716	0	+	G	G	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2368	2369	rs2441647	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2379	2380	rs3950657	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2395	2396	rs62028717	0	+	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2469	2470	rs2974781	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2634	2635	rs11510117	0	+	A	A	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2636	2637	rs11510118	0	+	G	G	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2642	2643	rs2949418	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2645	2646	rs62635284	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2655	2656	rs11510119	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2669	2670	rs62635285	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2810	2811	rs2462499	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2886	2887	rs2462498	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2978	2979	rs62635286	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	2980	2981	rs62028691	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3000	3001	rs12239753	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3016	3017	rs2691331	0	-	A	A	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3020	3021	rs12239425	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3022	3023	rs12239277	0	+	A	A	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3040	3041	rs62028689	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3164	3165	rs2691330	0	-	C	C	A/C/G/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3164	3165	rs28434453	0	-	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3164	3165	rs28532600	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3189	3190	rs2691329	0	-	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3223	3224	rs4951865	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3262	3263	rs4951866	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3286	3287	rs4951867	0	+	A	A	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3321	3322	rs2747970	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3335	3336	rs2592733	0	-	T	T	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3354	3355	rs28455646	0	-	C	C	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3370	3371	rs28461966	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3370	3371	rs4951868	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3419	3420	rs2981841	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3475	3476	rs4951869	0	+	T	T	A/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3526	3527	rs2974786	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3529	3530	rs7536480	0	+	C	C	C/T	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3530	3531	rs2691328	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3546	3547	rs4951870	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3591	3592	rs2691327	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3612	3613	rs2691326	0	-	C	C	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3638	3639	rs2691325	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3661	3662	rs7523129	0	+	T	T	G/T	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3675	3676	rs28719485	0	+	T	T	G/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3675	3676	rs7166048	0	-	T	T	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3691	3692	rs11490436	0	-	G	G	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3697	3698	rs11490238	0	+	G	G	C/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs28391190	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs28428499	0	+	C	C	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3700	3701	rs7164031	0	-	C	C	A/G	genomic	single	by-cluster,by-2hit-2allele	0	0	unknown	exact	3
585	chr1	3767	3768	rs2974788	0	+	A	A	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3767	3768	rs62028756	0	+	A	A	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3774	3775	rs2691324	0	-	G	G	C/T	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3797	3798	rs62530143	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3797	3798	rs7536681	0	+	C	C	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3808	3809	rs62530144	0	+	G	G	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3808	3809	rs7544137	0	+	G	G	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3834	3835	rs62530145	0	+	C	C	A/C	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3834	3835	rs7536753	0	+	C	C	A/C	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3842	3843	rs2592732	0	-	T	T	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3842	3843	rs62635296	0	+	T	T	C/T	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3843	3844	rs5940665	0	-	T	T	A/G	genomic	single	unknown	0	0	unknown	exact	3
585	chr1	3844	3845	rs7163793	0	-	C	C	A/G	genomic	single	by-cluster	0	0	unknown	exact	3
585	chr1	3888	3889	rs2758121
This article has been dead for over six months. Start a new discussion instead.