[Bioperl-l] Bioperl query....

Manju Rawat manju.rawat2 at gmail.com
Thu Sep 1 02:53:53 EDT 2011


Thanks For The Reply..
I have already seen this link..But I am confused.

I used to following code and run it...

my $in = Bio::SearchIO->new(-format => 'blast',
                -file => 'seqs.blast');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
    " gaps=",            $hsp->gaps,
            " Percent_id=", $hsp->percent_identity, "\n";
        }     } }    }}



and it showing me following output with an error that..


*Erro--*rArgument "" isn't numeric in numeric lt (<) at
/usr/local/share/perl/5.10.1/Bio/SearchIO/SearchResultEventBuilder.pm line
279, <GEN1> line 4113.

Query=NM_181451 Hit=ref|NM_181451.1| Length=1349 gaps=1 Percent_id=100
Query=NM_181451 Hit=ref|XM_002706247.1| Length=1345 gaps=13
Percent_id=93.8289962825279
Query=NM_181451 Hit=ref|NM_001098089.1| Length=1323 gaps=7
Percent_id=91.9123204837491
Query=NM_181451 Hit=ref|NM_001008415.1| Length=1211 gaps=5
Percent_id=94.9628406275805
Query=NM_181451 Hit=ref|XM_001251693.3| Length=1320 gaps=5
Percent_id=91.969696969697
Query=NM_181451 Hit=ref|NM_001097567.1| Length=1338 gaps=4
Percent_id=91.5545590433483
Query=NM_181451 Hit=gb|AY075103.1| Length=1334 gaps=1
Percent_id=91.304347826087
................
..........

Pl Find.whats the error i this code...

Thanks
Manju Rawat.


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