[Bioperl-l] length of hit->description

[Fields, Christopher J]

That is unusual.  The only recourse is to submit a bug report to Github and attach an example report giving the error.  My feeling is that this might be a change in the output for FASTA.

chris

On Jul 24, 2014, at 12:54 PM, Antony Vincent <antony.vincent.1 at ulaval.ca> wrote:

> Hello,
> 
> Thank you for the quick answer.
> 
> Here is a part of the code:
> #fasta parameters
> my $fh;  
> my $query = 'MyORF.tfa';
> my $library = "$library";                 
> my $fasta   = 'fasta35'; 
> 
> 
> # The fasta parsing part
> my $command = "$fasta -b 1 $query $library";
> 
> open $fh,"$command |" || die("cannot run fasta cmd of $command: $!\n");
> 
> my $searchio  = Bio::SearchIO->new(-format => 'fasta', -fh => $fh);
> while( my $result = $searchio->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') > $length*0.85) {
>        if ( $hsp->frac_conserved >= 0.65) {
> 
> 	
> 	print $hit->description(500), "\n";
> 	
> 
> 
> 				}
>            }
> 		}
> 	}  
> }
> 
> The correct result should be :
> repB	putative plasmid replication protein RepB
> 
> And I get:
> repB	putative plasmid replication protein R
> 
> Thank you,
> 
> Antony
> 
> Le 2014-07-24 à 13:48, Fields, Christopher J <cjfields at illinois.edu> a écrit :
> 
>> You’ll have to be more explicit.  What is the analysis (BLAST, FASTA, BLAT, etc)?  What is the expected result?  
>> 
>> Most of the above parsers will take the hit name as the first set of non-whitespace characters, and anything after that is put into the description.
>> 
>> chris
>> 
>> On Jul 24, 2014, at 12:04 PM, Antony03 <antony.vincent.1 at ulaval.ca> wrote:
>> 
>>> Hello,
>>> 
>>> When I use hit->description I get a truncated result like this:
>>> 
>>> repB putative plasmid replication protein R
>>> 
>>> I tried hit->description(500) and I get the same result.
>>> 
>>> Is there something wrong?
>>> 
>>> Thanks
>>> 
>>> 
>>> 
>>> --
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>> 
>