Re: get full hit descrption from blast output (xml)

[graff]

I want to help, but based on what you've posted, it's hard. First, you didn't post a complete XML file -- I have to wonder if there's anything else missing besides a bunch of close tags at the end of your sample data.

Then, your command line doesn't really give us enough info. What would be reasonable values for the "-n number_of_hits_to_keep" and "-b bit_score_cutoff" in order to get relevant results? Also, your command line uses a "-d" where I think the script is expecting a "-t".

And I'm sorry to seem picky, but you should be able to find an easy way to get your indention right (emacs? vi? some decent IDE or other programmer-savvy editor? perltidy?). Trust me, it really helps.

Anyway, I did manage to get the output you reported, but I'm a stranger to Bio::SearchIO, and I really can't tell what line or portion of the code actually has something to do with the "Hit_def" parameter in the xml file.

Just using a straightforward XPath extraction for "//Hit_def" on your (fixed) xml file does indeed return the full string you want - "43989.cce_0262 (Cyanothece ATCC 51142)".

In order to figure it out, I had to add this at the top:

use Data::Dumper 'Dumper';

Then step through it with the debugger until I got inside this block:

    while (my $hit = $result->next_hit) {

Then my next debugger command was:

p Data::Dumper::Dumper($hit)

Looking through the resulting output, I found the missing string -- see if you can find it too... Once you do, you should be able to figure out how to print it to your output file as desired:

$VAR1 = bless( {
                 '_hsps' => [
                              {
                                '-query_start' => 253,
                                '-algorithm' => 'BLASTX',
                                '-gaps' => '0',
                                '-hit_seq' => 'ITGAVCLMDYLEKVLEKLRELAQ
+KLIETLLGPQ',
                                '-hit_length' => '65',
                                '-query_length' => '508',
                                '-query_desc' => 'HKUN3Y301D9XQX',
                                '-query_frame' => -1,
                                '-rank' => 1,
                                '-hit_desc' => '43989.cce_0262 (Cyanot
+hece ATCC 51142)',
                                '-query_end' => 155,
                                '-hit_name' => 'gnl|BL_ORD_ID|1515029'
+,
                                '-identical' => '17',
                                '-query_name' => 'Query_1',
                                '-evalue' => '0.00664016',
                                '-score' => '92',
                                '-conserved' => '27',
                                '-hit_frame' => 0,
                                '-hsp_length' => '33',
                                '-query_seq' => 'LRGAICSMEHIEEALGKLKDW
+ARKLIELLLGPR',
                                '-hit_start' => '12',
                                '-homology_seq' => '+ GA+C M+++E+ L KL
+++ A+KLIE LLGP+',
                                '-hit_end' => '44',
                                '-bits' => '40.0466'
                              }
                            ],
                 '_iterator' => 0,
                 '_description' => '(Cyanothece ATCC 51142)',
                 '_significance' => '0.00664016',
                 '_query_length' => '508',
                 '_accession' => '1515029',
                 '_length' => '65',
                 '_psiblast_iteration' => '1',
                 '_name' => '43989.cce_0262',
                 '_rank' => 1,
                 '_algorithm' => 'BLASTX',
                 '_root_verbose' => 0,
                 '_hashes' => {
                                '0' => 1
                              },
                 '_hsp_factory' => bless( {
                                            'interface' => 'Bio::Searc
+h::HSP::HSPI',
                                            'type' => 'Bio::Search::HS
+P::GenericHSP',
                                            '_loaded_types' => {
                                                                 'Bio:
+:Search::HSP::GenericHSP' => 1
                                                               },
                                            '_root_verbose' => 0
                                          }, 'Bio::Factory::ObjectFact
+ory' )
               }, 'Bio::Search::Hit::GenericHit' );