Shell Programming and Scripting

>sample_1
FKGJGPOPOPOQA
ASDADWEEWERE
ASDAWEWQWRW
ASDASDASDASDD

>sample_1
DRTOWPFPOPOQA
ASDADWEEASDF
ASDADRTYWRW
ASDASDASDASDD

cat file_1
>sample_1
FKGJGPOPOPOQA
ASDADWEEWERE
ASDAWEWQWRW
ASDASDASDASDD

cat file_2
>sample_1
DRTOWPFPOPOQA
ASDADWEEASDF
ASDADRTYWRW
ASDASDASDASDD

perl -e ' ($file1, $file2) = @ARGV; $printed = 0; open F2, $file2; while (<F2>) { $h2{$_}++ }; $count2 = $.; open F1, $file1; while (<F1>) { if (! $h2{$_}) { print $_; $printed++; } } $count1 = $.; warn "\nRead $count1 lines from $file1 and $count2 lines from $file2.\nPrinted $printed lines found in $file1 but not in $file2\n\n" ' file_1 file_2 > file_3

cat file_3
FKGJGPOPOPOQA
ASDADWEEWERE
ASDAWEWQWRW

FKGJGPO
WERE
WEWQ

$ awk -F "" '
NR==FNR{a[NR]=$0;next} 
!/>/ { 
          split(a[FNR],b,""); 
          {     for (i=1;i<=NF;i++) {if ($i!=b[i]) printf b[i]}
                printf RS
          }
      } 
' file1 file2

FKGJGO
WERE
WEWQ

>sample_1
FKGJGPOPOPOQA
ASDADWEEWERE
ASDAWEWQWRW
ASDASDASDASDD

>sample_1
ASDFRPOPOPPWE
ASDADWEERTTY
ASDAPERTWRW
ASDASDASDASDD

FKGJG     OQA
        WERE
    WEWQ

FKGJG     OQA

FKGJGOQA

awk -F "" '
NR==FNR{a[NR]=$0;next}
!/>/ {
          split(a[FNR],b,"");
          {     for (i=1;i<=NF;i++) {printf ($i!=b[i])?b[i]:" "}
                printf RS
          }
      }
' file1 file2

FKGJG     OQA
        WERE
    W WQ