[Bioperl-l] Issue with Bio::SearchIO::psl (was: Bioperl bug 1977)

Chris Fields cjfields at uiuc.edu
Thu Apr 6 20:40:56 EDT 2006

I just committed a fix to Bio::SearchIO::psl.  It may take about 20  
minutes from now to update on CVS. This seems to work with or w/o the  
-w shebang flag on Mac OS X.

Let me know if you have more problems with it.


On Apr 6, 2006, at 3:19 AM, Albert Vernon Smith wrote:

> OK.  Neither you nor I put our shebang lines or the 'use' lines.   
> I'm always putting -w on the shebang line out of habit, and trying  
> to remove associated messages.  Makes things cleaner in the long  
> run.  I had always thought that -w was the same as 'use warnings',  
> but I've now learned it is not.  I don't get the message with 'use  
> warnings', so we are on the same page now.
> Thanks,
> -albert
> On 6.4.2006, at 04:28, Chris Fields wrote:
>> As it turns out, the script you sent me back (the one which you  
>> said was mine) gave me the answer.  It's the -w flag in the  
>> shebang line.  You had modified modified my script a bit by adding  
>> -w (I used 'use warnings' since -w gives a ton of debugging info  
>> on Windows).  I see the error popping up now on Mac (I haven't  
>> tried WinXP yet but will tomorrow).
>> I'll give it a closer look tomorrow.  I don't think the fix you  
>> suggested is the right one for now since it doesn't address the  
>> real problem (the parser doesn't 'see' the end of the report), but  
>> keep it in if it works for you.  Another workaround, w/o modifying  
>> Bio::SearchIO::psl, is to do this:
>> my $result = $parser->next_result;
>> while (my $hit = $result->next_hit) {
>> 	print $hit->name,"\n";
>> 	while (my $hsp = $hit->next_hsp) {
>> 		print "    ",$hsp->score,"\n";
>> 	}
>> }
>> which calls next_report only once.  I don't get the error with this.

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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