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]

In reply to Bio::Search::Hit::BlastHit unreturned results misformats csv output by hansoffate

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