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

Chris Fields cjfields at uiuc.edu
Thu Apr 6 00:28:12 EDT 2006

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  

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.


On Apr 4, 2006, at 10:15 AM, Albert Vernon Smith wrote:

> I deleted all of my bioperl installation, and reinstalled to be
> certain that this is a current issue.  Having done that, I am still
> seeing the issue.  I also updated IO::Handle to the most recent
> version, on the off chance that it was something coming from there.
> -albert
> On 1.4.2006, at 06:54, Chris Fields wrote:
>> Albert,
>> I had no problems with this on Mac OS X (I'm running from 10.4.5,
>> perl 5.8.6).  I noticed that several fixes were made in the last 6
>> months that would potentially fix this issue, including two which
>> involve newlines (that is what seems to be hanging things up
>> here).  Have you tried a full bioperl-live install to see if that
>> fixes it?
>> computer:~/searchio_test cjfields$ perl psl.pl
>> /usr/local/blat/db/hg17/hg17.2bit:chr5
>>     100.00
>> /usr/local/blat/db/hg17/hg17.2bit:chr21
>>     90.00
>> /usr/local/blat/db/hg17/hg17.2bit:chr5
>>     85.00
>> /usr/local/blat/db/hg17/hg17.2bit:chr13
>>     80.00
>> /usr/local/blat/db/hg17/hg17.2bit:chr7
>>     80.00
>> Chris
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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