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Torsten Seemann | 1 May 02:22
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Re: generate a fasta file from the blast report

> if i have the following script working on my blast report, can anyone plz
> tell me how can i generate a fasta format file of just the hits (subject)
> sequence.

Do you want the WHOLE subject sequence, or just the region that hit the query?

The hit is available as $hsp->hit_string();
http://doc.bioperl.org/bioperl-live/Bio/Search/HSP/GenericHSP.html#CODE11

The whole subject sequence would require the original Fasta input file.

By the way, are your questions for work related issues, or is this
your homework or assignment for a study course?

--Torsten
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Shameer Khadar | 1 May 13:36
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Help : Imagemaps using Bio::Graphics

Dear All,

I am trying to impliment a bioperl based program to generate a dynamic,
clickable image. I have used Dr. Lincoln Steins's code provided in
example3 at this URL :
http://stein.cshl.org/genome_informatics/BioGraphics/blast3.html seems to
be perfect for my purpose.

I need to add few modifications to the image. I reffered the Bio::Graphics
HOWTO,  Creating_Imagemaps documents and other old bio-perl list mails
(may be am missing something imp.. ? )  but I couldnt get a quick
solution, Thought I will ask about it to the experts for some tips and
tricks.

This is what I am looking for :

1. I need image of exactly same size and the scale (0.1k .. 0.9k) to be
changed according to length of the sequence. My sequence length is usually
in a range of 70 - 200.

2. I also need to make the image interactive / clickable on the various
blue bar as different hyperlink to NCBI / PDB using ID (This ids will be
used instead of name of the blast hits)

Many thanks in advance for your inputs,
--

-- 
Shameer Khadar
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
(Continue reading)

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Shameer Khadar | 1 May 18:04
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Re: Help : Imagemaps using Bio::Graphics

Dear Scot,

> There is a fair amount of documentation in the perldoc for
> Bio::Graphics::Panel under the section called 'Creating Imagemaps'; have
> you read that?

I agreed, but I couldnt the exact information I needed :( (may be I missed
something important).

>  Also, for changing the scale, that should happen
> automatically--have you tried yet?

I tried by changing the Lincoln's program eg: blast3.pl
my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>1000);
 to my
$full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>300);

But it had given me a smaller scale of length upto 300. I was looking for
an option where I need same width and height of given image and a dynamic
start and end values depending on length of my sequence. Since I couldnt
accomplish, I thought of getting some help from you guys. I think I need
to play a little bit with the value for reformat the scale to accomodate
my hits as well.

Thanks a lot for your inputs,
--

-- 
Shameer Khadar
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
(Continue reading)

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Shameer Khadar | 1 May 18:04
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Re: Help : Imagemaps using Bio::Graphics

Dear Scot,

> There is a fair amount of documentation in the perldoc for
> Bio::Graphics::Panel under the section called 'Creating Imagemaps'; have
> you read that?

I agreed, but I couldnt the exact information I needed :( (may be I missed
something important).

>  Also, for changing the scale, that should happen
> automatically--have you tried yet?

I tried by changing the Lincoln's program eg: blast3.pl
my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>1000);
 to my
$full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>300);

But it had given me a smaller scale of length upto 300. I was looking for
an option where I need same width and height of given image and a dynamic
start and end values depending on length of my sequence. Since I couldnt
accomplish, I thought of getting some help from you guys. I think I need
to play a little bit with the value for reformat the scale to accomodate
my hits as well.

Thanks a lot for your inputs,
--

-- 
Shameer Khadar
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
GKVK Campus, Bellary Road, Bangalore - 65, Karnataka - India
(Continue reading)

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Scott Cain | 1 May 16:04
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Re: Help : Imagemaps using Bio::Graphics

Hi Shameer,

There is a fair amount of documentation in the perldoc for
Bio::Graphics::Panel under the section called 'Creating Imagemaps'; have
you read that?  Also, for changing the scale, that should happen
automatically--have you tried yet?

Scott

On Tue, 2007-05-01 at 17:06 +0530, Shameer Khadar wrote:
> Dear All,
> 
> I am trying to impliment a bioperl based program to generate a dynamic,
> clickable image. I have used Dr. Lincoln Steins's code provided in
> example3 at this URL :
> http://stein.cshl.org/genome_informatics/BioGraphics/blast3.html seems to
> be perfect for my purpose.
> 
> I need to add few modifications to the image. I reffered the Bio::Graphics
> HOWTO,  Creating_Imagemaps documents and other old bio-perl list mails
> (may be am missing something imp.. ? )  but I couldnt get a quick
> solution, Thought I will ask about it to the experts for some tips and
> tricks.
> 
> This is what I am looking for :
> 
> 1. I need image of exactly same size and the scale (0.1k .. 0.9k) to be
> changed according to length of the sequence. My sequence length is usually
> in a range of 70 - 200.
>
(Continue reading)

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Chris Fields | 1 May 19:10
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Re: Pb makefile

Is there any reason you want to install bioperl 1.4 (which is over 3  
yrs old)?  The latest is v.1.5.2 (Dec. 2006); man page generation has  
been fixed for that version, which uses Module::Build.

The man page generation was turned off prior to 1.4, though I may be  
wrong.  Based on the Extutils::MakeMaker FAQ you should be able to  
prevent man page generation this way:

perl Makefile.PL INSTALLMAN1DIR=none INSTALLMAN3DIR=none

chris

On Apr 30, 2007, at 5:35 AM, Francoise.LECOMTE <at> biogemma.com wrote:

> Hi
> I try to install biopoerl1.4 on Tru64 plateform and I've got a message
> "make:line too long" when I run the command make install
> How can I solve it ? How disable man pages installaton in  
> Makefile.PL if
> it can sove this problem
>
> Best regards
>
> Françoise Lecomte
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Scott Cain | 1 May 21:50
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Re: Help : Imagemaps using Bio::Graphics

Perhaps if you provided some code and sample data we might be able to
help you better.

Scott

On Tue, 2007-05-01 at 21:34 +0530, Shameer Khadar wrote:
> Dear Scot,
> 
> > There is a fair amount of documentation in the perldoc for
> > Bio::Graphics::Panel under the section called 'Creating Imagemaps'; have
> > you read that?
> 
> I agreed, but I couldnt the exact information I needed :( (may be I missed
> something important).
> 
> >  Also, for changing the scale, that should happen
> > automatically--have you tried yet?
> 
> I tried by changing the Lincoln's program eg: blast3.pl
> my $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>1000);
>  to my
> $full_length = Bio::SeqFeature::Generic->new(-start=>1,-end=>300);
> 
> But it had given me a smaller scale of length upto 300. I was looking for
> an option where I need same width and height of given image and a dynamic
> start and end values depending on length of my sequence. Since I couldnt
> accomplish, I thought of getting some help from you guys. I think I need
> to play a little bit with the value for reformat the scale to accomodate
> my hits as well.
>
(Continue reading)

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Gathman, Allen | 2 May 01:10
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Problem with spliced_seq in BioPerl 1.5.2

Hi, all --

I've been using BioPerl 1.4 for a while; recently I installed 1.5.2, and
found that scripts that had been using spliced_seq are now broken.  Any
thoughts on what might be going on? 

Here's a sample script:

*********************************************

#!/usr/bin/perl -w

use strict;
use Bio::DB::GFF;

my $db  = Bio::DB::GFF-> new ( - adaptor => 'dbi::mysql',
                               -dsn        =>
'dbi:mysql:database=cc;host=localhost',
                               -fasta      => '/gbrowse/databases/cc'
                               );
$db->add_aggregator('transcript{CDS/mRNA}');
my $seg=$db->segment('ccin_Contig120');
my @genes=$seg->features(-types=>('transcript:GLEAN_alt'));

for my $gene (@genes) {
    my $gid = $gene->display_id;

    print STDERR "Gene is $gid\n";
    my $splgene = $gene->spliced_seq();
}
(Continue reading)

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Chris Fields | 2 May 02:27
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Re: Problem with spliced_seq in BioPerl 1.5.2

Can you file a bug on this?  Attach the script and maybe detail what  
data is loaded into your local MySQL database (if possible).

chris

On May 1, 2007, at 6:10 PM, Gathman, Allen wrote:

> Hi, all --
>
> I've been using BioPerl 1.4 for a while; recently I installed  
> 1.5.2, and
> found that scripts that had been using spliced_seq are now broken.   
> Any
> thoughts on what might be going on?
>
> Here's a sample script:
>
> *********************************************
>
> #!/usr/bin/perl -w
>
> use strict;
> use Bio::DB::GFF;
>
> my $db  = Bio::DB::GFF-> new ( - adaptor => 'dbi::mysql',
>                                -dsn        =>
> 'dbi:mysql:database=cc;host=localhost',
>                                -fasta      => '/gbrowse/databases/cc'
>                                );
> $db->add_aggregator('transcript{CDS/mRNA}');
(Continue reading)

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Shameer Khadar | 2 May 05:46
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Re: Help : Imagemaps using Bio::Graphics

Dear Scott,

Once thanks a lot for your inputs.

I am following same  data formats as in
http://stein.cshl.org/genome_informatics/BioGraphics/eg/blast_hits.txt
Only difference is instead of Hits, I will be using PFAMID/PDBID. Allt he
blue boxes (feature) should be clickable like a hot-spot/imagesmap images.
The purpose is to display these results in a web page.

I am using the program in Stein's Bio::Graphics example
http://stein.cshl.org/genome_informatics/BioGraphics/eg/blast3.pl

I need exactly same image as in
http://stein.cshl.org/genome_informatics/BioGraphics/fig3.png
only difference is I need the scale (0.1k - 0.9k) in a range of simple
1-XXX , here XXX depends on the length of the sequence input.

Many thanks for your help,

> Perhaps if you provided some code and sample data we might be able to
> help you better.
>
> Scott
>

--

-- 
Shameer Khadar
Lab (# 25) The Computational Biology Group
National Centre for Biological Sciences (TIFR)
(Continue reading)

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Gmane