[Bioperl-l] limiting E value - Argument "e-134" isn't numeric?

[Joseph Bedell]

Nice.

>-----Original Message-----
>From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
>Sent: Tuesday, April 06, 2004 10:00 AM
>To: Joseph Bedell
>Cc: Nandita Mullapudi;
>Subject: RE: [Bioperl-l] limiting E value - Argument "e-134" isn't
numeric?
>
>or in one line... =)
>
>$E =~ s/^e/1e/i;
>
>In Bio::SearchIO we automagically reformat the evalue for you.  I don't
>remember when we introduced this feature but it is definitely should be
>1.4.0.
>
>-jason
>On Tue, 6 Apr 2004, Joseph Bedell wrote:
>
>> Hi Nandita,
>>
>> You must be using NCBI-BLAST. NCBI has a problem in that they don't
>> include the '1' before E-values less than or equal to 1e-100. So, any
>> e-value you get back needs to be checked for '^e' and have a '1'
added
>> on so it evaluates as a number.
>>
>> $E = "1" . $E if $E =~ /^e/;
>>
>> Joey
>>
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Joseph A Bedell, Ph.D.
>> Director, Bioinformatics
>> Orion Genomics, LLC
>> 4041 Forest Park Ave.
>> St. Louis, MO 63108
>> Office:(314)615-6979; Fax:(314)615-6975
>> Mobile:(314)518-1343
>> http://www.oriongenomics.com
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>
>> >-----Original Message-----
>> >From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
>> >bounces at portal.open-bio.org] On Behalf Of Nandita Mullapudi
>> >Sent: Tuesday, April 06, 2004 8:10 AM
>> >To: bioperl-l at portal.open-bio.org
>> >Subject: [Bioperl-l] limiting E value - Argument "e-134" isn't
numeric?
>> >
>> >I am using the following line in my script to limit e-values, and I
>> >remember having used it before without error messages, but now...
>> >
>> >the line is:  if ($hit_significance < 0.001 && $i < 3)
>> >                      { print ...}
>> >
>> >and the error message I get is
>> >
>> >Argument "e-134" isn't numeric in numeric lt (<) at try-exclude.pl
line
>> 31,
>> >         <GEN871> line 12023 (#1)
>> >(W numeric) The indicated string was fed as an argument to an
operator
>> >     that expected a numeric value instead.  If you're fortunate the
>> >message
>> >     will identify which operator was so unfortunate.
>> >
>> >any quick insight appreciated. :)
>> >-Nandita
>> >_______________________________________________
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>> >Bioperl-l at portal.open-bio.org
>> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
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>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu