Shell Programming and Scripting

read_2 10 15
read_3 5 8
read_1 4 10
.
.
.

++read_1
AFSFAFHAKSJFHAKSJFHAKJSFHAFHASJKFHAS
++read_2
ASDFASJFOASUFRIEUIEWOUIEOWUIOEWUIEWFSFSJDHGJDSKHGSKDJHG
++read_3
UTWETEWTWETEWTEWTEF
.
.

++read_1
AFSXXXXXXXJFHAKSJFHAKJSFHAFHASJKFHAS
++read_2
ASDFASJFOXXXXXXEUIEWOUIEOWUIOEWUIEWFSFSJDHGJDSKHGSKDJHG
++read_3
UTWEXXXXWETEWTEWTEF
.
.

awk 'NR==FNR{a["++"$1]=$2;b["++"$1]=$3}
NR>FNR&&a[RS$1]{print RS$1"\n"substr($2,1,a[RS$1]-1)gensub(/./,"X","g",substr($2,a[RS$1],b[RS$1]-a[RS$1]+1))substr($2,b[RS$1]+1)}' ref RS="++read" file
++read_1
AFSXXXXXXXJFHAKSJFHAKJSFHAFHASJKFHAS
++read_2
ASDFASJFOXXXXXXEUIEWOUIEOWUIOEWUIEWFSFSJDHGJDSKHGSKDJHG
++read_3
UTWEXXXXWETEWTEWTEF

#!/usr/bin/perl
use strict;

my %ref_h;
my (@refdata,@ar);
my ($start,$end,$format,$col);

open(RF,"<","reffile") or  die "Fail-$!\n";
while (<RF>) {
chomp;
@refdata=split;
$ref_h{$refdata[0]}=[$refdata[1],$refdata[2]]
}
close(RF);

open(DF,"<","datafile") or die "Fail-$!\n";
while (<DF>){
        chomp;
        if (/^\+\+/) {
        ($col=$_)=~s/\++//g;
        next unless exists $ref_h{$col} ;
        print "$_\n";
        $start=$ref_h{$col}[0];
        $end=$ref_h{$col}[1];
        next;
        }
        next unless $start>0;
        $format="A".($start-1)." x".($end-$start+1)." A*";
        @ar=unpack($format, $_);
        ($ar[1],$ar[2])=("X" x ($end-$start+1),$ar[1]);
        print @ar,"\n";
        $start=0;$end=0;
}
close(DF);

#!/usr/bin/perl

my %ref_h;
my (@refdata,@ar);
my ($start,$end,$format,$col);

open(RF,"<","reffile") or  die "Fail-$!\n";
while (<RF>) {
chomp;
@refdata=split;
push (@{$refdata[0]},$refdata[1],$refdata[2]);
$ref_h{$refdata[0]}=\@{$refdata[0]}
}
close(RF);

open(DF,"<","input_file.txt") or die "Fail-$!\n";
while (<DF>){
        chomp;
        if (/^\>/) {
        ($col=$_)=~s/\>//g;
        next unless exists $ref_h{$col} ;
        print "$_\n";
        next;
        }
        $index=$#{$col};
        for ($k=0;$k<=$index;$k++) {
        $start=$ref_h{$col}[$k];
        $end=$ref_h{$col}[++$k];
        $format="A".($start-1)." x".($end-$start+1)." A*";
        @ar=unpack($format,$_);
        ($ar[1],$ar[2])=("X" x ($end-$start+1),$ar[1]);
        ($_="@ar")=~s/\s//g;
        undef @ar;
        }
        print $_,"\n";
        $start=0;$end=0;$index=0;
}
close(DF);

substr($_,($start-1),($end-$start+1))="X" x ($end-$start);

#!/usr/bin/perl

my %ref_h;
my (@refdata,@ar);
my ($start,$end,$format,$col);

open(RF,"<","reffile") or  die "Fail-$!\n";
while (<RF>) {
chomp;
@refdata=split;
push (@{$refdata[0]},$refdata[1],$refdata[2]);
$ref_h{lc $refdata[0]}=\@{$refdata[0]}
}
close(RF);

open(DF,"<","/tmp/input_file.txt") or die "Fail-$!\n";
while (<DF>){
        chomp;
        if (/^\>/) {
        ($col=$_)=~s/\>//g;
        next unless exists $ref_h{lc $col} ;
        print "$_\n";
        next;
        }
        $index=$#{$col};
        for ($k=0;$k<=$index;$k++) {
        $start=$ref_h{lc $col}[$k];
        $end=$ref_h{lc $col}[++$k];
        substr($_,($start-1),($end-$start+1))="X" x ($end-$start);
        }
        print $_,"\n";
        $start=0;$end=0;$index=0;
}
close(DF);