I think you want something more like this. I'm guessing a little on some of the code. Otherwise I factored out all the common code, which as far as I can tell is everything but the url. 

sub blast_hu_parse {
  my($maid,$maid_dir) = @_;
  my $url_hu = "http://hu_seq/";
  blast_parse($maid,$maid_dir,$url_hu);
}

sub blast_hd_parse {
  my($maid,$maid_dir) = @_;
  my $url_hd = "http://hd_seq/";  
  blast_parse($maid,$maid_dir,$url_hd);
}

sub blast_parse{
    my($maid,$maid_dir,$url) = @_;

    my $h_file = get($url.$maid);
    my $ltvec_small = $maid_dir.$maid."Ltvec_small.fa";
    
    #what is $hu where is it declared?
    #open ($hu);
    #what is $in  where is it declared 
    my $seq=<$in>;
    close($in);   
    open (my $hu, ">".$maid.".fa");
    print $hu ">$maid\n$seq";
    close($hu);

    # syntax
    # bl2seq -p blastn -i nucleotide1 -j nucleotide2 -F F -D 1 
    my $command = "bl2seq -p blastn -i $ltvec_small -j $h_file -F F -D
+ 
+1";
    print $command,"\n";
    open OUTPUT, '>',  "$maid_dir\\".$maid."_bl2seq.out" ;
    STDOUT->fdopen( \*OUTPUT, 'w');
    system($command); 
    bl2seq_parse();
}

[download]

update added some comment on the file handling stuff, which appears to have some errors, after looking over the original again

In reply to Re: how can I combine into one method by thunders
in thread how can I combine into one method by lomSpace

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