[Bioperl-l] [Bioperl]problem with E-value

Sendu Bala bix at sendu.me.uk
Wed Jan 17 09:17:42 EST 2007


lidaof wrote:
> Hi Sendu,
>  
> Thanks for your reply!
> the blast result and my .pl file were attached with this mail as a 
> single compressed file(the first attachment)
> and on the machine installed bioperl 1.5.2_100
> the exactly wrong message like"
> Argument "1e" isn't numeric in numeric comparison (<=>) at 
> /usr/lib/perl5/site_perl
> /5.8.5/Bio/SearchIO/blast.pm line 661, <GEN1> line 50.
> Argument "1e" isn't numeric in numeric comparison (<=>) at 
> /usr/lib/perl5/site_perl
> /5.8.5/Bio/SearchIO/blast.pm line 661, <GEN1> line 78.
> "
> and on the machine installed bioperl 1.5.1,no wrong message
> but the output result is Different!!!
> and the different result are attached as the second attachment

Thanks for those. Can you describe in detail exactly how you generated 
the blast report?

The problem is that Bioperl is completely mis-parsing the results. No 
version of Bioperl is able to handle your blast report, because the 
blast parser seems to expect there to be alignments for those 'Sequences 
producing significant alignments'.

Until the parser is fixed (assuming your blast report is valid), let me 
make it clear: do NOT use Bioperl to parse your blast report - the 
results are TOTALLY WRONG.


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