hansoffate has asked for the wisdom of the Perl Monks concerning the following question:

For the most part, my script below works to generate a csv file. However, sometimes it doesn't return a result, which causes my csv file to be incorrectly aligned. A sample input sequence which causes alignment issues is below.

Thanks for the help,
-Hans 

 
use strict;
use Bio::Tools::Run::RemoteBlast;
use Getopt::Std;

my $usage = "\nusage: <script_name> <input_file> <output_file>\n".
         "Creates a CSV file with query_name, hit_name, score, and exp
+ect\n\n".
         "-b Y or N          If Y, it will produce the blastoutput for
+ each sequence query; Defaults N\n\n";

our($opt_b);
getopts('b:') or die $usage;
if(!defined($opt_b)) { $opt_b = 'N'; }

my $prog = 'blastp';
my $db = 'nr';
my $e_val = '1e-2';
my $v = 1;

my $infile = shift or die $usage;
my $outfile = shift or die $usage;

open OUT, ">$outfile" or die $usage;
print OUT "Query_Name,Description,Hit_Name,Score,Expect\n";

my $remoteBlast = Bio::Tools::Run::RemoteBlast->new(-prog => $prog,
                                                    -data => $db,
                                                    -readmethod => 'Se
+archIO',
                                                    -expect => 100);
my $v = 1;

#my $str = Bio::SeqIO->new(-file=>'smallinput.fna', -format => 'fasta'
+ );
my $str = Bio::SeqIO->new(-file=> $infile, -format => 'fasta' );

$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Arabidopsis [
+ORGN]';
###animals not plants


while( my $input = $str->next_seq()) {
  my $r = $remoteBlast->submit_blast($input);

  print STDERR "waiting..." if ($v > 0);
  while(my @rids = $remoteBlast->each_rid) {
    foreach my $rid (@rids) {
      my $rc = $remoteBlast->retrieve_blast($rid);
      if(!ref($rc)) {
        if($rc < 0 ) {
          $remoteBlast->remove_rid($rid);
        }
        print STDERR "." if ($v > 0);
        sleep 5;
      } else {
        my $result = $rc->next_result();

        #### save the output
        if($opt_b eq 'Y') {
          my $filename = $result->query_name()."\.out";
          $remoteBlast->save_output($filename);
        }
        $remoteBlast->remove_rid($rid);
        print "\nQuery Name: ", $result->query_name(), " retrieved\n";
        while (my $hit = $result->next_hit) {
          next unless ($v > 0);
          #print OUT $result->query_name().",".$result->query_descript
+ion().",".$hit->name().",";
          if(defined($hit)) {
            print OUT $result->query_name().",".$hit->name().",";
          } else {
            print OUT "\n";
          }
          while (my $hsp = $hit->next_hsp) {
            #print OUT $hsp->score().",".$hsp->expect()."\n";
            if(defined($hsp)) {
              print OUT $hsp->score().",".$hsp->expect().",".$result->
+query_description()."\n";
            } else {
              print OUT "\n";
            }
          }
        }
      }
    }
  }
}

close OUT;

[download]
inputfile 
>gi|117625301|ref|YP_854502.1| hydrogenase 2 protein HybA [Escherichia
+ coli APEC O1]
MNRRNFIKAASCGALLTGALPSVSHAAAENRPPIPGSLGMLYDSTLCVGCQACVTKCQDINFPERNPQGE
QTWSNNDKLSPYTNNIIQVWTSGTGVNKDQEENGYAYIKKQCMHCVDPNCVSVCPVSALKKDPKTGIVHY
DKDVCTGCRYCMVACPYNVPKYDYNNPFGALHKCELCNQKGVERLDKGGLPGCVEVCPAGAVIFGTREEL
MAEAKKRLALKPGSEYHYPRQTLKSGDTYLHTVPKYYPHLYGEKEGGGTQVLVLTGVPYENLDLPKLDDL
STGARSEHVQHTLYKGMMLPLAVLAGLTVLVRRNTKNDHHDGGDDHES

[download]

Replies are listed 'Best First'.
Re: Bio::Search::Hit::BlastHit unreturned results misformats csv output
by jrsimmon (Hermit) on Jun 30, 2009 at 17:50 UTC
    How sure are you that the methods you are having trouble with return undef and not '', 0, -1, etc when a problem is encountered?
[reply]
      I'm not that sure, however, this is what the next_hit() module does according to cpan.< 
       Title   : next_hit
 Usage   : while( $hit = $result->next_hit()) { ... }
 Function: Returns the next available Hit object, representing potenti
+al
           matches between the query and various entities from the dat
+abase.
 Returns : a Bio::Search::Hit::HitI object or undef if there are no mo
+re.
 Args    : none

      [download]
      The same is true for next_hsp(). Therefore, I thought if I threw I check to see if they are defined, it would only print if they are. Is this incorrect?
[reply]
[d/l]
        I'm not in the least familiar with the modules you're using, so I may not be much help...that said, I'd definitely confirm that the behavior of the module you're using. Something like 
        open(DBG, ">$some_log_file") or die;
while (my $hit = $result->next_hit) {
  next unless ($v > 0);
  #print OUT $result->query_name().",".$result->query_description().",
+".$hit->name().",";
  if(defined($hit)) {
    my $debug_qry = $result->query_name();
    my $debug_hit = $hit->name();
    print DBG "$debug_qry\t$debug_hit\t$hit\n";
    print OUT $result->query_name().",".$hit->name().",";
  } else {
    print OUT "\n";
  }

  while (my $hsp = $hit->next_hsp) {
    #print OUT $hsp->score().",".$hsp->expect()."\n";
    if(defined($hsp)) {
      my $debug_score = $hsp->score();
      my $debug_expect = $hsp->expect();
      my $debug_qry_desc = $result->query_description();
      print DBG "$debug_score\t$debug_expect\t$debug_qry_desc\t$hsp\n"
+;
      print OUT $hsp->score().",".$hsp->expect().",".$result->query_de
+scription()."\n";
    } else {
      print OUT "\n";
    }
  }
}

        [download]
        You could use Data::Dumper too, but that's probably overkill for what you need at this point. The point is that you need to verify whether you're getting a bad return from the method or whether you're handling a proper return badly.
[reply]
[d/l]

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