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Jason Stajich | 1 Nov 2005 23:47
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Re: Genbank parser

Bio::SeqIO parses genbank files.
There is a spliced_seq method to splice CDS sequence out from a set of
  http://bioperl.org/Core/Latest/faq.html#Q5.5

See the HOWTOs for sequence introduction and feature and annotation  
introduction.
http://bioperl.org/Core/Latest/modules.html

and particularly the tutorial as well:
http://bioperl.org/Core/Latest/bptutorial.html

-jason

On Oct 30, 2005, at 8:35 PM, Bingshan Li wrote:

> Hi All,
>
> I am new to Bioperl and recently found it has a lot of useful  
> modules. I wrote a perl script to extract all protein sequences and  
> corresponding coding sequences from Genbank files. But I found some  
> bugs and it's hard to make sue my script is bug free after several  
> revision. I am wondering if there are some modules and specific  
> functions to use to fulfill my requirement. Does anybody have  
> similar code to share with? Most bugs come from multiple segments  
> of coding sequences and some cds sequences are on the minus strand.
>
> Thanks a lot!
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
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Bingshan Li | 2 Nov 2005 01:00
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Re: Bio::Align::DNAStatistics ka/ks calculation bugs?

Thanks, Jason, for this reply and the other for Ganbank parser. For  
Yn00, can we pass a slice of alignment to it so that I can calculate  
ka/ks for sliding windows? I ran PAML as a stand alone program but  
never used it in perl script.

Thanks a lot!

-bs

On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote:

> I suggest Codeml and YN00 - I assume you are only doing this for  
> pairwise comparisons and not along a tree?
>
> The dnastats  module calculates Nei-Gojobori so it will be  
> different, but shouldn't be that different so something must be  
> wrong with your code or the module's method.  Maybe you can post a  
> bug to bugzilla.open-bio.org with a clear example of where it is  
> going wrong and we'll take a look.
>
> I would just use YN00 for most pairwise - you can parse it with  
> Bio::Tools::Phylo::PAML and automate running it with  
> Bio::Tools::Run::Phylo::PAML::Yn00
>
>
> -jason
> On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote:
>
>
>> Hi all,
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Jason Stajich | 1 Nov 2005 23:45
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Re: Bio::Align::DNAStatistics ka/ks calculation bugs?

I suggest Codeml and YN00 - I assume you are only doing this for  
pairwise comparisons and not along a tree?

The dnastats  module calculates Nei-Gojobori so it will be different,  
but shouldn't be that different so something must be wrong with your  
code or the module's method.  Maybe you can post a bug to  
bugzilla.open-bio.org with a clear example of where it is going wrong  
and we'll take a look.

I would just use YN00 for most pairwise - you can parse it with  
Bio::Tools::Phylo::PAML and automate running it with  
Bio::Tools::Run::Phylo::PAML::Yn00

-jason
On Oct 31, 2005, at 5:54 PM, Bingshan Li wrote:

> Hi all,
>
> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio  
> but I found the result is very different from the output by yn00 in  
> PAML 3.14. I applied "calc_KaKs_pair" function on two sequences to  
> test it. The difference is pretty big (for one case it gave ka/ 
> ks=1.35 while yn00 gave 0.37). Does anybody have same experience?  
> Is there any other methods I can use to calculate ka/ks ratios? I  
> will also use it to calculate ka/ks in sliding windows.
>
> Thanks a lot!
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
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Torsten Seemann | 2 Nov 2005 00:08
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Re: Bio::Align::DNAStatistics ka/ks calculation bugs?

> I used Bio::Align::DNAStatistics module to calculate ka/ks ratio but  
> I found the result is very different from the output by yn00 in PAML  
> 3.14. I applied "calc_KaKs_pair" function on two sequences to test  
> it. The difference is pretty big (for one case it gave ka/ks=1.35  
> while yn00 gave 0.37). Does anybody have same experience? Is there  
> any other methods I can use to calculate ka/ks ratios? I will also  
> use it to calculate ka/ks in sliding windows.

I don't know anything about the details of those ratios, but I do notice
that 
	1.35 = (1/2) / 0.37 

if that helps. 

--

-- 
Torsten Seemann <torsten.seemann <at> infotech.monash.edu.au>
Victorian Bioinformatics Consortium
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Jason Stajich | 2 Nov 2005 01:08
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Re: Bio::Align::DNAStatistics ka/ks calculation bugs?

That's right.   see the PAML HOWTO - $dna_aln can be slices of an  
alignment.

# set the alignment object
$kaks_factory->alignment($dna_aln);

# run the KaKs analysis
my ($rc,$parser) = $kaks_factory->run();
my $result = $parser->next_result;
my $MLmatrix = $result->get_MLmatrix();

On Nov 1, 2005, at 7:00 PM, Bingshan Li wrote:

> Thanks, Jason, for this reply and the other for Ganbank parser. For  
> Yn00, can we pass a slice of alignment to it so that I can  
> calculate ka/ks for sliding windows? I ran PAML as a stand alone  
> program but never used it in perl script.
>
> Thanks a lot!
>
> -bs
>
> On Nov 1, 2005, at 4:45 PM, Jason Stajich wrote:
>
>
>> I suggest Codeml and YN00 - I assume you are only doing this for  
>> pairwise comparisons and not along a tree?
>>
>> The dnastats  module calculates Nei-Gojobori so it will be  
>> different, but shouldn't be that different so something must be
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chen li | 2 Nov 2005 06:29
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Bio::SeqIO HOWTO

Hi folks,

 Here is one script copied from the Bio::SeqIO HOWTO:

     use Bio::SeqIO;
     my $usage = "getaccs.pl file format\n";
     my $file = shift or die $usage;
     my $format = shift or die $usage;

     my $inseq = Bio::SeqIO->new('-file'  => "<$file",
              '-format' => $format );
     while (my $seq = $inseq->next_seq) {
           print $seq->accession_number,"\n";
     }
     exit;

I have a small file called mouse.fasta kept in the
same directory. My question is that  how does the
script know to read in mouse.fasta? Where should I
make a small modification in the script?

Thanks,

Li

		
__________________________________ 
Yahoo! FareChase: Search multiple travel sites in one click.
http://farechase.yahoo.com
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Barry Moore | 2 Nov 2005 07:00
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RE: Bio::SeqIO HOWTO

Li-

You don't need to modify the script.  It is written to accept the
filename and format on the command line like this:  perl getaccs.pl
mouse.fasta fasta.

Barry

> -----Original Message-----
> From: bioperl-l-bounces <at> portal.open-bio.org [mailto:bioperl-l-
> bounces <at> portal.open-bio.org] On Behalf Of chen li
> Sent: Tuesday, November 01, 2005 10:30 PM
> To: bioperl-l <at> bioperl.org
> Subject: [Bioperl-l] Bio::SeqIO HOWTO
> 
> Hi folks,
> 
>  Here is one script copied from the Bio::SeqIO HOWTO:
> 
>      use Bio::SeqIO;
>      my $usage = "getaccs.pl file format\n";
>      my $file = shift or die $usage;
>      my $format = shift or die $usage;
> 
>      my $inseq = Bio::SeqIO->new('-file'  => "<$file",
>               '-format' => $format );
>      while (my $seq = $inseq->next_seq) {
>            print $seq->accession_number,"\n";
>      }
>      exit;
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Edward WIJAYA | 2 Nov 2005 02:49
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Re: Bio::SeqIO HOWTO


On Wed, 02 Nov 2005 13:29:54 +0800, chen li <chen_li3 <at> yahoo.com> wrote:

> Hi folks,
>
Hi

> I have a small file called mouse.fasta kept in the
> same directory. My question is that  how does the
> script know to read in mouse.fasta? Where should I
> make a small modification in the script?
>

http://search.cpan.org/src/BIRNEY/bioperl-1.4/Bio/Tools/GuessSeqFormat.pm

It's in Bio::Tools::GuessSeqFormat.

--

-- 
Regards,
Edward WIJAYA
SINGAPORE
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Brian Osborne | 2 Nov 2005 10:42

Re: noob Bio::DB::Biblio problem

Chihiro,

What happens when you set the access mode to "soap" or "eutils" rather than
to "biofetch"?

Brian O.

On 10/31/05 9:19 AM, "Chihiro Yamada" <cy200 <at> gen.cam.ac.uk> wrote:

> Hiya folks,
> 
> I'm trying to use the Bio::DB::Biblio::biofetch module to get references
> by ID, but I'm having a problem...
> 
> If I run this code...
> 
> use Bio::Biblio;
> my $biblio = new Bio::Biblio (-access => 'biofetch');
> my $ref = $biblio->get_by_id('15519282');
> 
> I get the error message:
> 
> ------------- EXCEPTION  -------------
> MSG: retrieval type pipeline unsupported
> 
> STACK
> Bio::DB::Biblio::biofetch::get_seq_stream
> /opt/csw/share/perl/site_perl/Bio/DB/Biblio/biofetch.pm:237
> STACK
> Bio::DB::DBFetch::get_Stream_by_id
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t-nakazato | 2 Nov 2005 10:54
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Re: noob Bio::DB::Biblio problem

Hi,

If you don't need to use "biofetch" protocol, try "eutils".

use Bio::Biblio;
my $biblio = new Bio::Biblio (-access => 'eutils');  # biofetch -> eutils
my $ref = $biblio->get_by_id('15519282');

And, you can write with perl one liner (on command line).

perl -MBio::Biblio -le 'print Bio::Biblio->new(-access => "eutils")->get_by_id("1551982")'

Takeru

> Hiya folks,
> 
> I'm trying to use the Bio::DB::Biblio::biofetch module to get references
> by ID, but I'm having a problem...
> 
> If I run this code...
> 
> use Bio::Biblio;
> my $biblio = new Bio::Biblio (-access => 'biofetch');
> my $ref = $biblio->get_by_id('15519282');
> 
> I get the error message:
> 
> ------------- EXCEPTION  -------------
> MSG: retrieval type pipeline unsupported
>
(Continue reading)

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Gmane