#!/usr/bin/perl -w

# Parsing BLAST reports with BioPerl's Bio::SearchIO module;
# Recover single HSP (the first one);
# No filtering options;

#use strict;
use Bio::SearchIO;


# Prompt the user for the file name if it's not an argument;
# NOTE: BLAST file must be in text (not html) format;
if (! $ARGV[0])
{
   $usage = "./blast_parsing_single.pl BLASTREPORT";
   print "Usage is '$usage' or.....\n";
   print "What is the BLAST file to parse? ";

   # Get input and remove the newline character at the end;
   chomp ( $inFile = <STDIN>);
}
else
{
   $inFile = $ARGV[0];
}

$report = new Bio::SearchIO( -format => 'blast',
                                -file   => "$inFile"   );

# Prints the header for the columns;
print "Query_Name\tQuery_Acc\tQuery_Len\tHit_Acc\tHit_Desc\tHit_Signif\n";


# Go through BLAST reports              
while( $result = $report->next_result ) 
{
    #print $result->query_name . "\t" ;
    $counter = 0;

   # Just takes the first hit
    while ( $hit = $result->next_hit)
    {    if ($counter == 0)
    
         {
         
            # Print tab-delimited data;
            		print $result->query_name, "\t";
            		print $result->query_accession, "\t";
            		print $result->query_length, "\t";
            		print $hit->accession, "\t";
            		print $hit->description, "\t";
            		print $hit->significance, "\t";
            
            $counter++;
		  }
    }
   
    print "\n";
}