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Hilmar Lapp | 2 May 2005 00:41
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Re: Bio::DB::Query

Carito,

sorry I didn't have time to get back to you earlier. The documentation 
of many modules is certainly far from complete, and most if not all 
modules could certainly benefit a lot from examples. The fact that 
documentation is sparse in many cases is not due to ignorance or 
oversight though, but simply due to lack of time, or in other words 
lack of volunteers.

As for modifying records after they are read by SeqIO and before they 
are stored in the database, the perfect mechanism for this with support 
built into load_seqdatabase.pl is to write a sequence processor. Have 
you read the documentation under the --pipeline option in 
load_seqdatabase.pl? It references the respective modules in bioperl 
that the framework is built upon which will have more documentation. I 
use this every day with great success for my own projects.

As for the rest of your email, be sure to note one thing. 
Bioperl/biosql/bioperl-db is open source - you didn't pay for it, did 
you? - and has been written by volunteers, i.e., people who didn't stop 
at complaining but went on to volunteer their unpaid time and made this 
world a better place for themselves and everybody else too by making an 
effort to correct the issues they found.

	-hilmar

On Thursday, April 21, 2005, at 12:57  PM, carito vargas wrote:

> Hi
>
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Edward Chuong | 2 May 2005 23:13
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PAML parsing: standard error?

Hi,

Has parsing the standard errors for pairwise comp been implemented
yet? Can't seem to figure out how to retrieve them.

(if getSE = 1, the bottom of the file would look like this)

pairwise comparison, codon frequencies: F3x4.

2 (PM_BWp0020A12f/1-633) ... 1 (mouse/1-630)
lnL =-1299.951893
  0.88536  2.62235  0.89353
SEs for parameters:
  0.08133  0.51260  0.19693

t= 0.8854  S=   178.0  N=   443.0  dN/dS= 0.8933  dN= 0.2854  dS= 0.3194
dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 1)
dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 2)

Thanks!
-Ed
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Jason Stajich | 3 May 2005 04:31
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Re: PAML parsing: standard error?

Nope, it's not parsed.  feel free to add it and post a patch...

On May 2, 2005, at 5:13 PM, Edward Chuong wrote:

> Hi,
>
> Has parsing the standard errors for pairwise comp been implemented
> yet? Can't seem to figure out how to retrieve them.
>
> (if getSE = 1, the bottom of the file would look like this)
>
> pairwise comparison, codon frequencies: F3x4.
>
>
> 2 (PM_BWp0020A12f/1-633) ... 1 (mouse/1-630)
> lnL =-1299.951893
>   0.88536  2.62235  0.89353
> SEs for parameters:
>   0.08133  0.51260  0.19693
>
> t= 0.8854  S=   178.0  N=   443.0  dN/dS= 0.8933  dN= 0.2854  dS= 
> 0.3194
> dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 1)
> dN = 0.28536 +- 0.03182   dS = 0.31943 +- 0.05807 (by method 2)
>
> Thanks!
> -Ed
>
> _______________________________________________
> Bioperl-l mailing list
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Diego Riano | 3 May 2005 09:55
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Problem retrieving sequences from NCBI

Hello,
I have a small problem.
I have a script to retrieve sequences from ncbi.  If there are specified
coordinates, then the script only retrieves the corresponding region
from the sequence.
The input of the script is a file (IN) with a list of accession numbers
and an optional pair of coordinates (start-end), and the user can
specified the output format (default is fasta).
When a specific region was specified, there is a secondary accesion
number:
REGION: start..end
The problem that I have is that for some sequences I found in the
output, for the secondary ac:
REGION: ?
Any idea why this could happen?
###############################################
    while(my $line=<IN>){
	chomp $line;
	my ($id,$coords)=split(/\t/,$line);
	my $fetch="http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$id&retmode=text";
	if(defined($format) && $format ne ""){
	    $fetch.="&rettype=$format";
	}
	else{
	    $fetch.="&rettype=fasta";
	}
	if (defined($coords)){
	    my ($start,$end)=split(/-/,$coords);
	    $fetch.="&seq_start=$start&seq_stop=$end";
	}
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James Gilbert | 3 May 2005 17:04
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v5.005 in INSTALL


Hi,

A user emailed me to say that our Bio::Index modules don't work with 
Perl 5.005, and that a lot of others don't either because they have 
"use warnings". It says in the INSTALL file that 5.005 is OK. Should we 
change the INSTALL file to a later version of Perl, or fix 5.005 
compatability? (He had to use 5.005 on a particular machine because it 
is required by his SRS installation.)

Personally I'd go with 5.6.1 as a minimum. I like "use base", which is, 
I think, a 5.6.1 feature.

This is what we have in the INSTALL:

o SYSTEM REQUIREMENTS

  - perl 5.005 or later*.

  - External modules: Bioperl uses functionality provided in other
    Perl modules.  Some of these are included in the standard perl
    package but some need to be obtained from the CPAN site. The
    list of external modules is included at the bottom of
    this INSTALL document.

    The CPAN Bioperl Bundle (Bundle::BioPerl) makes installation
    of these external modules easy. Simply install the bundle
    using your CPAN shell and all necessary modules will be installed.
    See THE BIOPERL BUNDLE, below.
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Hilmar Lapp | 3 May 2005 17:38
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Re: v5.005 in INSTALL

I ran an informal survey on this a couple days ago, you can check the 
archive for the results. The bottom line is that most people appear to 
use 5.6.1 or 5.8.x, but for instance FlyBase <at> Harvard still uses 5.005 
although apparently they are in the process of upgrading. MacOSX 10.2 
comes with 5.6.0 and Apple never updated it (in 10.2).

	-hilmar

On Tuesday, May 3, 2005, at 08:04  AM, James Gilbert wrote:

>
> Hi,
>
> A user emailed me to say that our Bio::Index modules don't work with 
> Perl 5.005, and that a lot of others don't either because they have 
> "use warnings". It says in the INSTALL file that 5.005 is OK. Should 
> we change the INSTALL file to a later version of Perl, or fix 5.005 
> compatability? (He had to use 5.005 on a particular machine because it 
> is required by his SRS installation.)
>
> Personally I'd go with 5.6.1 as a minimum. I like "use base", which 
> is, I think, a 5.6.1 feature.
>
> This is what we have in the INSTALL:
>
> o SYSTEM REQUIREMENTS
>
>  - perl 5.005 or later*.
>
>  - External modules: Bioperl uses functionality provided in other
(Continue reading)

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Waibhav Tembe | 3 May 2005 17:40

Megablast Ouput

Hello List,

I was wondering if BioPerl parse routines from BLAST output could be 
used for megablast output as well (assuming that the display format for 
megablast output has been set to BLAST like output).

Secondly, if the output display format (-m parameter) for blastall is 
changed, is it still possible to use BioPerl blast output parsers to 
extract hits/HSPs/Evalue etc?

Thanks.

Regards,

-waibhav
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Jason Stajich | 3 May 2005 17:48
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Re: Megablast Ouput

Bio::SearchIO::blast will parse MEGABLAST output the -D 0 and -D 2 
formats.

-jason

On May 3, 2005, at 11:40 AM, Waibhav Tembe wrote:

> Hello List,
>
> I was wondering if BioPerl parse routines from BLAST output could be 
> used for megablast output as well (assuming that the display format 
> for megablast output has been set to BLAST like output).
>
> Secondly, if the output display format (-m parameter) for blastall is 
> changed, is it still possible to use BioPerl blast output parsers to 
> extract hits/HSPs/Evalue etc?
>
> Thanks.
>
> Regards,
>
> -waibhav
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l <at> portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
--
Jason Stajich
(Continue reading)

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Waibhav Tembe | 3 May 2005 18:02

Re: Megablast Ouput

Thanks for the quick reply. Another question:

If I don't care about the statistics of the the hits, but only need the 
local alignments and no. of gaps/mismatches, is using megablast and 
blast with the following parameters equivalent?

blastall -p blastn -d DB -F f -q -1 -r 1 -G 2 -E 1 -W 7 -I T -e 10000000 
-i Input -o Output

megablast -d DB -F f -q -1 -r 1 -G 2 -E 1 -W 28 -I T -m 0 -D 2 -n T -R 
T  -i Input -o Output

1. I tried to set E value large in BLAST to get all possible hits.
2. Since megablast computes a hash for every 4 base pairs, I selected 
W=28 which (I think) should match W=7 for blastn

Any suggestions/comments/criticism welcome.

I have to blast more than 100 short sequences of length approx 50bp and 
need to get local alignment scores using a modest linux box. I observed 
that megablast runs very fast as compared to BLAST. So I am curious to 
know if I will miss any hits using megablast instead of blast. As I 
mentioned, I don't care about the statistics.

Thanks.

Jason Stajich wrote:

> Bio::SearchIO::blast will parse MEGABLAST output the -D 0 and -D 2 
> formats.
(Continue reading)

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michael watson (IAH-C | 4 May 2005 14:33
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Error writing out EMBL

Hi

I'm on bioperl-1.5.

I get this when writing out an EMBL file:

FT
/gene_id="Bio::Annotation::SimpleValue=HASH(0x858d688)"
FT
/note="Bio::Annotation::SimpleValue=HASH(0x8595360)"

My code is:

use Bio::Perl;
use Bio::SeqIO;
use Bio::Seq;
use Bio::SeqFeature::Generic;

my $seq = Bio::Seq->new(-display_id => 'test',
			-seq => "ACGTACGTACGTACGT");

my $gene = "test gene";

my $gene_feat = Bio::SeqFeature::Generic->new(-start   => 2, 
					      -end     => 5,
					      -primary => 'CDS',
					      -tag => {gene_id => $gene,
						       note => 'test
gene'});
(Continue reading)

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Gmane