将下列代码存入文件get_position_seq.pl，然后可以使用perl get_position_seq.pl -h获得帮助！

#! /usr/bin/perl

use Bio::SeqIO;

use Getopt::Long;

GetOptions(

        'Position|P=s'           => $inputfile1,

        'Seq|s=s'               => \$inputfile2,

        'O=s'                   => \$inputfile3,

        'help|h!'              => \$help,

);

my @good;

my $h=0;$k=0;

if($help){

print "###################################################################\n";

print "usage perl get_position_seq.pl -p position.file -s seq.file -o getseq.file\n";

print "######input position file is the format:\n" ;

print "######gene_ID    start(0 as start)    get_length\n";

print "Options:\n";

print "    -p:the input position file\n";

print "    -s:the fasta sequence file\n";

print "    -o:the output sequence file\n";

}else{

open (IN1, "<$inputfile1")|| die "cannot open $inputfile:$!";

open (OUT, ">$inputfile3")|| die "cannot open $inputfile:$!";

while (<IN1>){

@tmp=split;

       push @position, [@tmp];

}

my $ina = Bio::SeqIO->new(-file => $inputfile2, -format => 'fasta');

while(my $obj = $ina->next_seq()){

         my $id = $obj->id;

         my $seq = $obj->seq;

  $xulie[$k++]="$id $seq\n";

}

foreach(@xulie){

@tmp=split;

push @Mat, [@tmp];

}

for($i=0;$i<=($#position);$i++){

 for($j=0;$j<=($#Mat);$j++){

   if($position[$i][0] eq $Mat[$j][0]){

        $good[$h][0]=">$position[$i][0]";

      $good[$h][1]=substr($Mat[$j][1],$position[$i][1],$position[$i][2]);

print OUT "$good[$h][0]\n$good[$h][1]\n";

      $h++;

last;

}

}

}

close IN1;

close OUT;

}