#!/usr/bin/perl
use strict;
use Data::Dumper;
use warnings;
use Bio::SeqIO;
use IO::Handle;
use Bio::SearchIO;
use Bio::AlignIO;
use LWP::Simple;
use IO::String;
use Bio::SearchIO::Writer::TextResultWriter;


my @results_arr = get_info();
open( my $out,">C:/Documents and Settings/mgavi.brathwaite/Desktop/bl2
+seq_parsing/out.txt"); 
print $out  "$results_arr[0]", "\n", "$results_arr[1]";
sub get_info{
my $maid = '10890';
my $maid_dir = "C:/Documents and Settings/mgavi.brathwaite/Desktop/bl2
+seq_parsing";
my $in = new Bio::SearchIO(-format => 'blast',
                           -file   => $maid_dir."/".$maid."aln_hu.aln"
+,
                           -report_type => 'blastn');
open(my $out, ">$maid_dir/".$maid."aln_hu_parsed.out");
#my $out = Bio::AlignIO->newFh(-file => ">$maid_dir/".$maid."aln_hu_pa
+rsed.out",
#                                -format => 'clustalw' );
my $result=$in->next_result;
my($hu_aln,$hu_mismatches);
# Get info about the first hit
my $hit = $result->next_hit;
my $name = $hit->name;
# get info about the first hsp of the first hit
my $hsp = $hit->next_hsp;
# get the alignment object
my $aln = $hsp->get_aln;
#my $percent_id = $hsp->percent_identity;
#my $aln_length = $hsp->length('total');
my @mismatches = $hsp->seq_inds('query','nomatch');
my $aln_str="";
# access the alignment string 
my $strIO=IO::String->new($aln_str);
#  write the string alignio in clustalw format
my $alnio = Bio::AlignIO->new(-format => 'clustalw', -fh=>$strIO);
# now the actual alignment string is accessable for printing or in thi
+s case moving to a db table
$alnio->write_aln($aln);
$hu_aln=$aln_str;
$hu_mismatches = scalar @mismatches;
print $out $hu_mismatches, "\n",$hu_aln;
return ($hu_aln, $hu_mismatches);
}
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