Hello wise monks!

I am trying to parse an xml file like the one below using the following script, and everything works well except that I cannot get the full hit description (the "Hit_def" parameter in this xml format).

What I want that output to read is "43989.cce_0262 (Cyanothece ATCC 51142)", but my output only has "(Cyanothece ATCC 51142)". I played around a bit and found that if I put non-numerical text infront of this information, then I get the entire hit description. However, I'd like to be able to retrieve it without modifying the xml file. Any suggestions?

Here is a sample of the xml input

<?xml version="1.0"?>
<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://ww
+w.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
<BlastOutput>
  <BlastOutput_program>blastx</BlastOutput_program>
  <BlastOutput_version>BLASTX 2.2.27+</BlastOutput_version>
  <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejan
+dro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, an
+d David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new gen
+eration of protein database search programs&quot;, Nucleic Acids Res.
+ 25:3389-3402.</BlastOutput_reference>
  <BlastOutput_db>/Applications/blast-2.2.27+/db/COG_Nov2012/protein.s
+equences.v9.0</BlastOutput_db>
  <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
  <BlastOutput_query-def>HKUN3Y301D9XQX</BlastOutput_query-def>
  <BlastOutput_query-len>508</BlastOutput_query-len>
  <BlastOutput_param>
    <Parameters>
      <Parameters_matrix>BLOSUM62</Parameters_matrix>
      <Parameters_expect>10</Parameters_expect>
      <Parameters_gap-open>11</Parameters_gap-open>
      <Parameters_gap-extend>1</Parameters_gap-extend>
      <Parameters_filter>L;</Parameters_filter>
    </Parameters>
  </BlastOutput_param>
  <BlastOutput_iterations>
    <Iteration>
      <Iteration_iter-num>1</Iteration_iter-num>
      <Iteration_query-ID>Query_1</Iteration_query-ID>
      <Iteration_query-def>HKUN3Y301D9XQX</Iteration_query-def>
      <Iteration_query-len>508</Iteration_query-len>
      <Iteration_hits>
        <Hit>
          <Hit_num>1</Hit_num>
          <Hit_id>gnl|BL_ORD_ID|1515029</Hit_id>
          <Hit_def>43989.cce_0262 (Cyanothece ATCC 51142)</Hit_def>
          <Hit_accession>1515029</Hit_accession>
          <Hit_len>65</Hit_len>
          <Hit_hsps>
            <Hsp>
              <Hsp_num>1</Hsp_num>
              <Hsp_bit-score>40.0466</Hsp_bit-score>
              <Hsp_score>92</Hsp_score>
              <Hsp_evalue>0.00664016</Hsp_evalue>
              <Hsp_query-from>155</Hsp_query-from>
              <Hsp_query-to>253</Hsp_query-to>
              <Hsp_hit-from>12</Hsp_hit-from>
              <Hsp_hit-to>44</Hsp_hit-to>
              <Hsp_query-frame>-1</Hsp_query-frame>
              <Hsp_hit-frame>0</Hsp_hit-frame>
              <Hsp_identity>17</Hsp_identity>
              <Hsp_positive>27</Hsp_positive>
              <Hsp_gaps>0</Hsp_gaps>
              <Hsp_align-len>33</Hsp_align-len>
              <Hsp_qseq>LRGAICSMEHIEEALGKLKDWARKLIELLLGPR</Hsp_qseq>
              <Hsp_hseq>ITGAVCLMDYLEKVLEKLRELAQKLIETLLGPQ</Hsp_hseq>
              <Hsp_midline>+ GA+C M+++E+ L KL++ A+KLIE LLGP+</Hsp_midl
+ine>
            </Hsp>
          </Hit_hsps>
        </Hit>
[download]

and here is the perl script:

#!/usr/local/bin/perl

# Usage information
#Usage: $0 -i <BLAST-report-file> -o <output-file> -n <number-of-top-h
+its> -b <min_bit_score>
# -t <trashed.output_queries_without_hits> 

use strict;
use warnings;
use Bio::SearchIO;
use Getopt::Std;#needed for flagging parameters

sub main{

my %opt;
#note: colons after letter mean the flag expects an argument
getopt('i:o:n:b:t:', \%opt);

print "Parsing the BLAST result ...\n";
my $in = Bio::SearchIO->new(-format => 'blastxml', -file => $opt{i});
open (OUT,">$opt{o}") or die "Cannot open $opt{o}: $!";
open (OUT2,">$opt{t}") or die "Cannot open $opt{t}: $!";
open (OUT3, ">$opt{o}.header") or die "Cannot open $opt{o}.header: $!"
+;


# print the header info for tab-deliminated columns
print OUT "query_name\tquery_length\taccession_number\tsubject_length\
+tsubject_description\tE value\tbit score\tframe\tquery_start\t";
print OUT "query_end\thit_start\thit_end\t%_conserved\t%_identical\n";

print OUT2 "query_name\tquery_length\taccession_number\tsubject_length
+\tsubject_description\tE value\tbit score\tframe\tquery_start\t";
print OUT2 "query_end\thit_start\thit_end\t%_conserved\t%_identical\n"
+;


# extraction of information for each result recursively
while ( my $result = $in->next_result ) {

    #prints query info for reads WITHOUT hits into -t ="bad" file
       if ( $result->num_hits == 0 ) {
        print OUT2 $result->query_description . "\t";
        print OUT2 $result->query_length . "\t";
        print OUT2 "No hits found\n";
        
        }
    else {
        my $count = 0;
        # process each hit recursively
        while (my $hit = $result->next_hit) {



            #prints query info for reads WITH hits BELOW bit-score inp
+ut value into -t = "bad" file
            if ( $hit->bits < $opt{b}) {
                   print OUT2 $result->query_description . "\t";
                print OUT2 $result->query_length . "\t";
                print OUT2 "below bit score\n";}
            #prints query and other info for reads WITH hits ABOVE bit
+-score input into -o = "good" file
            elsif (    $hit->bits >= $opt{b}) {
                   print OUT $result->query_description . "\t";
                   print OUT3 $result->query_description . "\n";
                print OUT $result->query_length . "\t";
                print OUT $hit->accession . "\t";
                   print OUT $hit->length . "\t";
                print OUT $hit->description . "\t";
                print OUT $hit->significance . "\t";
                print OUT $hit->bits . "\t";
                
                my $hspcount = 0;
            
                # process the top HSP for the top number of hits (user
+ defined) into -o file
                while (my $hsp = $hit->next_hsp) {
                    if ($hit->bits >= $opt{b}) {
                        print OUT "\t\t\t\t\t\t\t", if ($hspcount > 0)
+;
                            print OUT $hsp->query->frame . "\t";
                        print OUT $hsp->start('query') . "\t" . $hsp->
+end('query'). "\t";
                        print OUT $hsp->start('hit') . "\t" . $hsp->en
+d('hit') . "\t";
                        printf OUT "%.1f" , ($hsp->frac_conserved * 10
+0);
                        print OUT "%\t";
                        printf OUT "%.1f" , ($hsp->frac_identical * 10
+0);
                           print OUT "%\n";
                           $hspcount++;
                        }

                    }
                    
                }
            $count++;
            # flow control for the number of hits needed
            last if ($count == $opt{n});

        }
        
        }
      
}

close OUT;
close OUT2;

}
main();
print " DONE!!!\n";
[download]

and what I put into the command line:

and here is the output I get from "goodoutputfile.txt"

query_name    query_length    accession_number    subject_length    su
+bject_description    E value    bit score    frame    query_start    
+query_end    hit_start    hit_end    %_conserved    %_identical
HKUN3Y301D9XQX length=508 xy=1636_1159 region=1 run=R_2012_03_16_06_53
+_48_    508    1515029    65    (Cyanothece ATCC 51142)    0.00664016
+    40.0466    0    155    253    12    44    81.8%    51.5%
[download]