php read and updating value on file from another file -

i have 2 files (a.vcf , ref1.vcf) a.vcf this:

#chrom  pos id  ref alt qual    filter  info    format 1   5   .     c   222 .   indel;is=6,0.111111;dp=54;vdb=1.384012e-01;af1=0.5;ac1=1;dp4=2,3,1,4;mq=32;fq=10.8;pv4=1,0.38,0.00012,0.00052   gt:pl:gq    0/1:45,0,147:47 2   7   .   g   t   222 .   dp=106;vdb=1.997151e-13;rpb=-2.402409e+00;af1=1;ac1=2;dp4=1,1,44,58;mq=20;fq=-275;pv4=1,1,0.0029,1  gt:pl:gq    1/1:255,248,0:99 3   15  .     g   222 .   dp=106;vdb=2.982598e-04;rpb=-2.402409e+00;af1=1;ac1=2;dp4=1,1,44,58;mq=20;fq=-266;pv4=1,1,0.003,1   gt:pl:gq    1/1:255,239,0:99 4   11  .   t     222 .   dp=85;vdb=3.949915e-01;af1=1;ac1=2;dp4=0,0,29,44;mq=22;fq=-247  gt:pl:gq    1/1:255,220,0:99 

ref1.vcf :

#chrom  pos id  ref alt 1   5   ref12345      c 2   15  ref45673      g 3   25  ref67893    c   t 4   35  ref66663    c   

i want change heading of file corresponds reference a.vcf ref1.vcf. thus, initially:

id = . ref = alt = c qual = 222 

i want this:

id = ref12345 ref = alt = c qual = 222 

but no change happens. whether there mistake code?

<?php     $datasnp = "a.vcf";     $handlesnp = fopen($datasnp, "r");         if ($handlesnp)         {             while (($linesnp = fgets($handlesnp, 4096)) !== false)             {                 $linesnp = explode("\t", $linesnp);                 //removing first '#'                 if (!empty($linesnp[0][0]) && $linesnp[0][0] != '#')                 {                     $new_datasnp[] = $linesnp;                 }             }             if (!feof($handlesnp))             {                 echo "error: unexpected fgets() fail\n";             }             fclose($handlesnp);         }         //update 'pos', not working         for($i = 0 ; $i < count($new_datasnp); $i++)         {             echo '<pre>';             print("chrom = ".$new_datasnp[$i][0]. "\n");             print("position = ".$new_datasnp[$i][1]. "\n");             $file = "ref1.vcf";              $handle = fopen($file, "r");             if ($handle)             {                 while (($line = fgets($handle, 4096)) !== false)                 {                     $line = explode("\t", $line);                      if(($line[1] == $new_datasnp[$i][1]) && ($line[3] == $new_datasnp[$i][3]) && ($line[4] == $new_datasnp[$i][4]))                     {                         $new_datasnp[$i][2] = $line[2];                         break;                     }                 }                 if (!feof($handle))                 {                     echo "error: unexpected fgets() fail\n";                 }                 fclose($handle);             }                    print("id = ".$new_datasnp[$i][2]. "\n");                 print("ref = ".$new_datasnp[$i][3]. "\n");                 print("alt = ".$new_datasnp[$i][4]. "\n");          } ?> 

this code simple, confused find faults. there can me?

it's simple: fgets not cut off new-line character \n @ end of each line. so, $line[4] contains new-line character, while $new_datasnp[$i][4] not.

replace

$line = explode("\t", $line); 

with

$line = explode("\t", trim($line));