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Dave Messina | 1 Dec 11:14
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Re: [Bug 2937] Strand in fasta35 output does not seem to be parsed

Hi Mick,

Did you try running the test case that you had originally attached to the bug report? Or is the below from
different code and a diffrent fasta output file?

In any case, I'll need to look at the fasta35 output file and the parse2.pl you ran in order to reproduce and
fix this -- could you please open a new bug report and attach them to it?

Thanks,
Dave

On Nov 30, 2009, at 17:49, michael watson (IAH-C) wrote:

> Hi Dave
> 
> Just got round to looking at this.
> 
> In bioperl-1.6.0, the strand didn't get parsed, but the module only warned about something:
> 
> --------------------- WARNING ---------------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i
-O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> ---------------------------------------------------
> 
> However, in the bioperl-live I just downloaded, this had turned into a full-on stack trace:
> 
> ------------- EXCEPTION -------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i
-O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> STACK Bio::SearchIO::fasta::next_result /usr/local/bioperl-live_301109//Bio/SearchIO/fasta.pm:1347
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Emanuele Osimo | 1 Dec 19:05
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Statistics: how to obtain the p value of a T test

Hello everyone,
I'm trying to get the p value of a statistic made with Statistics::TTest
I cannot find this function: I can find if the null hypothesis is rejected
at a certain confidence level, but I cannot make the script show me the
actual p value.
Do you know other scripts that can do that?

Thanks
Emanuele
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Chris Fields | 1 Dec 20:25
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Fwd: [Utilities-announce] NCBI E-Utility Policy Change

I'll be adjusting the requisite parameters as indicated below.  I'm reluctant to include a time-based
limit on submissions (NCBI wants a max of 100 requests at peak hours), but it may become necessary if they
request it.

chris

Begin forwarded message:

> From: <utilities-announce <at> ncbi.nlm.nih.gov>
> Date: December 1, 2009 12:59:34 PM CST
> To: <utilities-announce <at> ncbi.nlm.nih.gov>
> Subject: [Utilities-announce] NCBI E-Utility Policy Change
> Reply-To: utilities-announce <at> ncbi.nlm.nih.gov
> 
> As part of an ongoing effort to ensure efficient access to the Entrez Utilities (E-utilities) by all
users, NCBI has decided to change the usage policy for the E-utilities effective June 1, 2010. Effective
on June 1, 2010, all E-utility requests, either using standard URLs or SOAP, must contain non-null values
for both the &tool and &email parameters. Any E-utility request made after June 1, 2010 that does not
contain values for both parameters will return an error explaining that these parameters must be
included in E-utility requests.
>  
> The value of the &tool parameter should be a URI-safe string that is the name of the software package,
script or web page producing the E-utility request.
>  
> The value of the &email parameter should be a valid e-mail address for the appropriate contact person or
group responsible for maintaining the tool producing the E-utility request.
>  
> NCBI uses these parameters to contact users whose use of the E-utilities violates the standard usage
policies described
athttp://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html#UserSystemRequirements.
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Mark A. Jensen | 2 Dec 03:27
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test test test

MAJ
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Ocar Campos | 2 Dec 03:59
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Re: test test test

test test test test back

O'car Campos C.
Bioinformatics Engineering Student.
University of Talca.
Chile.

2009/12/1 Mark A. Jensen <maj <at> fortinbras.us>

> MAJ
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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Mark A. Jensen | 2 Dec 04:08
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Re: test test test

I love when people are paying attention!
  ----- Original Message ----- 
  From: Ocar Campos 
  To: Mark A. Jensen ; Bioperl Mailing List. 
  Sent: Tuesday, December 01, 2009 9:59 PM
  Subject: Re: [Bioperl-l] test test test

  test test test test back

  O'car Campos C.
  Bioinformatics Engineering Student.
  University of Talca.
  Chile.

  2009/12/1 Mark A. Jensen <maj <at> fortinbras.us>

    MAJ
    _______________________________________________
    Bioperl-l mailing list
    Bioperl-l <at> lists.open-bio.org
    http://lists.open-bio.org/mailman/listinfo/bioperl-l
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Roopa Raghuveer | 2 Dec 13:07
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Remote blast

Hello everyone,

I have a problem. I am new to Bioperl. I am working on RNAi tool wherein a
cgi script was written which connects to NCBI blast using remote blast
program,i.e.,

The input sequence given in the html page is taken as input and Remote blast
is performed on this based on the code for Remote blast.But,I have a problem
in the Remote blast code.

My code goes like this

@compseqs=blastcode($in{'Inputseq'});

sub blastcode
{
$input1= $_[0];

open(NUC,'>',$nuc);
print NUC $input1;
close(NUC);

 my $prog = 'blastn';
 my $db   = 'refseq_rna';
 my $e_val= '1e-10';
 my $organism= 'Trypanosoma Brucei';

$gb = new Bio::DB::GenBank;

 my @params = ( '-prog' => $prog,
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Vipin Singh | 2 Dec 06:24
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Problems with installation

Dear Sir/Madam,
I have not been able to install bioperl on my Windows 32 machine despite
repeated attempts. I have tried both Active Perl and Strwaberry perl but
both do not seem to work.
I have followed the instruction given at
-- http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows

Please guide.
Thanks,
Vipin.
Vipin Singh,
Senior Research Fellow,
Centre for Cellular and Molecular Biology,
Hyderabad - 500007
India.
contact - 91-040-27192778
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Scott Cain | 2 Dec 15:18
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Re: Problems with installation

Hello Vipin,

"do not seem to work" doesn't give us much to go on; can you tell us
what happened?

Scott

On Wed, Dec 2, 2009 at 12:24 AM, Vipin Singh <ashvip <at> gmail.com> wrote:
> Dear Sir/Madam,
> I have not been able to install bioperl on my Windows 32 machine despite
> repeated attempts. I have tried both Active Perl and Strwaberry perl but
> both do not seem to work.
> I have followed the instruction given at
> -- http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
>
> Please guide.
> Thanks,
> Vipin.
> Vipin Singh,
> Senior Research Fellow,
> Centre for Cellular and Molecular Biology,
> Hyderabad - 500007
> India.
> contact - 91-040-27192778
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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Mark A. Jensen | 2 Dec 15:18
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Re: Problems with installation

Hi Vipin--
We need some more information; your commands, error messages you received.
Thanks, 
Mark
----- Original Message ----- 
From: "Vipin Singh" <ashvip <at> gmail.com>
To: <bioperl-l <at> lists.open-bio.org>
Sent: Wednesday, December 02, 2009 12:24 AM
Subject: [Bioperl-l] Problems with installation

> Dear Sir/Madam,
> I have not been able to install bioperl on my Windows 32 machine despite
> repeated attempts. I have tried both Active Perl and Strwaberry perl but
> both do not seem to work.
> I have followed the instruction given at
> -- http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
> 
> Please guide.
> Thanks,
> Vipin.
> Vipin Singh,
> Senior Research Fellow,
> Centre for Cellular and Molecular Biology,
> Hyderabad - 500007
> India.
> contact - 91-040-27192778
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
(Continue reading)

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Gmane