gmod-ajax

[Gmod-ajax] error by runing prepare-refseqs.pl

[Anja F. <fri...@ho...>]

From: fri...@ho...
To: gmo...@li...
Subject: error by runing prepare-refseqs.pl
Date: Wed, 29 Sep 2010 16:32:22 +0200








Hi all, 

I tried to run:

    

    >bin/prepare-refseqs.pl --conf taro.json --refs 1


    but I get:

Can't call method "name" on an undefined value at bin/prepare-refseqs.pl line 72.

Any idea?

Cheers, 
Anja 		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Mitch S. <mit...@be...>]

  Hi,

prepare-refseqs.pl is trying to get a reference sequence (chromosome, 
contig, scaffold, or whatever you have) out of the database.  But it's 
not getting back what it expected to get.

I randomly chose "1" as the name of the reference sequence in the 
example I sent you; I don't know how your reference sequences are 
named.  Are they chromosomes, or scaffolds, or something else?  And how 
are they named?  Is there a reference sequence called "1"?

The intended usage of prepare-refseqs.pl is for you to put a list of 
reference sequence names on the command line, as the values of the 
"--refs" argument.  For example,  if you have 3 scaffolds named scaf1, 
scaf2, and scaf3, your prepare-refseqs.pl command would look like this:

bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

In order for that to work, those sequences should already have been 
loaded into your database.

Hope this helps,
Mitch

On 09/29/2010 07:51 AM, Anja Friedrich wrote:
>
>
> ------------------------------------------------------------------------
> From: fri...@ho...
> To: gmo...@li...
> Subject: error by runing prepare-refseqs.pl
> Date: Wed, 29 Sep 2010 16:32:22 +0200
>
> Hi all,
>
> I tried to run:
>
> >bin/prepare-refseqs.pl --conf taro.json --refs 1
>
> but I get:
>
> Can't call method "name" on an undefined value at 
> bin/prepare-refseqs.pl line 72.
>
> Any idea?
>
> Cheers,
> Anja
>
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
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>
>
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
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Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Anja F. <fri...@ho...>]

Hi Mitch, 

thanks for the reply.
My reference sequence is lemna minor, I have it in gbk, fasta or gff format. 

Anja

Date: Wed, 29 Sep 2010 11:29:02 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
    E-Mail-Text
  
  
    Hi,

    

    prepare-refseqs.pl is trying to get a reference sequence
    (chromosome, contig, scaffold, or whatever you have) out of the
    database.  But it's not getting back what it expected to get.

    

    I randomly chose "1" as the name of the reference sequence in the
    example I sent you; I don't know how your reference sequences are
    named.  Are they chromosomes, or scaffolds, or something else?  And
    how are they named?  Is there a reference sequence called "1"?

    

    The intended usage of prepare-refseqs.pl is for you to put a list of
    reference sequence names on the command line, as the values of the
    "--refs" argument.  For example,  if you have 3 scaffolds named
    scaf1, scaf2, and scaf3, your prepare-refseqs.pl command would look
    like this:

    

    bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

    

    In order for that to work, those sequences should already have been
    loaded into your database.

    

    Hope this helps,

    Mitch

    

    On 09/29/2010 07:51 AM, Anja Friedrich wrote:
    
      
      

      

      From: fri...@ho...

      To: gmo...@li...

      Subject: error by runing prepare-refseqs.pl

      Date: Wed, 29 Sep 2010 16:32:22 +0200

      

      
      
      Hi all, 

      

      I tried to run:

      

      >bin/prepare-refseqs.pl --conf taro.json --refs 1

      

      but I get:

      

      Can't call method "name" on an undefined value at
      bin/prepare-refseqs.pl line 72.

      

      Any idea?

      

      Cheers, 

      Anja
      
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
      
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

    
    
 		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Anja F. <fri...@ho...>]

Hi, 

I loaded the lemna data with bp_seqfeature_load.pl into the database and wanted to use bin/prepare-refseqs.pl for the reference sequence. But I get:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find SO or SOFA in the database!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::sofa_id /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
STACK: Bio::DB::Das::Chado::new /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
STACK: bin/prepare-refseqs.pl:115
-----------------------------------------------------------
Could not open database: 
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: unable to find SO or SOFA in the database!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::sofa_id /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
STACK: Bio::DB::Das::Chado::new /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
STACK: bin/prepare-refseqs.pl:115
-----------------------------------------------------------

How can that be? I thought if I use Bio-SeqFeature-Store I dont need a database like Chado to store the data? Is there somewhere a description where I can read more about it and reference sequences?

Anja
Date: Wed, 29 Sep 2010 11:29:02 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
    E-Mail-Text
  
  
    Hi,

    

    prepare-refseqs.pl is trying to get a reference sequence
    (chromosome, contig, scaffold, or whatever you have) out of the
    database.  But it's not getting back what it expected to get.

    

    I randomly chose "1" as the name of the reference sequence in the
    example I sent you; I don't know how your reference sequences are
    named.  Are they chromosomes, or scaffolds, or something else?  And
    how are they named?  Is there a reference sequence called "1"?

    

    The intended usage of prepare-refseqs.pl is for you to put a list of
    reference sequence names on the command line, as the values of the
    "--refs" argument.  For example,  if you have 3 scaffolds named
    scaf1, scaf2, and scaf3, your prepare-refseqs.pl command would look
    like this:

    

    bin/prepare-refseqs.pl --conf taro.json --refs scaf1,scaf2,scaf3

    

    In order for that to work, those sequences should already have been
    loaded into your database.

    

    Hope this helps,

    Mitch

    

    On 09/29/2010 07:51 AM, Anja Friedrich wrote:
    
      
      

      

      From: fri...@ho...

      To: gmo...@li...

      Subject: error by runing prepare-refseqs.pl

      Date: Wed, 29 Sep 2010 16:32:22 +0200

      

      
      
      Hi all, 

      

      I tried to run:

      

      >bin/prepare-refseqs.pl --conf taro.json --refs 1

      

      but I get:

      

      Can't call method "name" on an undefined value at
      bin/prepare-refseqs.pl line 72.

      

      Any idea?

      

      Cheers, 

      Anja
      
------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
      
_______________________________________________
Gmod-ajax mailing list
Gmo...@li...
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

    
    
 		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Mitch S. <mit...@be...>]

  You're right that if you use Bio::DB::SeqFeature::Store then you don't 
need to use chado.  But it looks like the config file you're using with 
prepare-refseqs.pl might still refer to Bio::DB::Das::Chado?  If you 
change that to Bio::DB::SeqFeature::Store in the config file, then that 
should help.

Mitch

On 09/30/2010 02:13 AM, Anja Friedrich wrote:
> Hi,
>
> I loaded the lemna data with bp_seqfeature_load.pl into the database 
> and wanted to use bin/prepare-refseqs.pl for the reference sequence. 
> But I get:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
> Could not open database:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: unable to find SO or SOFA in the database!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw 
> /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::DB::Das::Chado::sofa_id 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482
> STACK: Bio::DB::Das::Chado::new 
> /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147
> STACK: bin/prepare-refseqs.pl:115
> -----------------------------------------------------------
>
> How can that be? I thought if I use Bio-SeqFeature-Store I dont need a 
> database like Chado to store the data? Is there somewhere a 
> description where I can read more about it and reference sequences?
>
> Anja

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Anja F. <fri...@ho...>]

My bad, I created the config file long time ago and forgot to have alook into it again ;(
By the way, where did you get the code for the colours in the css file from? Wikipedia is using different ones... and can JBrowse display any colour? As I have to display 12 small motifs I'm running out of colours...
Thanks for your help

Anja
Date: Thu, 30 Sep 2010 02:20:44 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
  
  
    You're right that if you use Bio::DB::SeqFeature::Store then you
    don't need to use chado.  But it looks like the config file you're
    using with prepare-refseqs.pl might still refer to
    Bio::DB::Das::Chado?  If you change that to
    Bio::DB::SeqFeature::Store in the config file, then that should
    help.

    

    Mitch

    

    On 09/30/2010 02:13 AM, Anja Friedrich wrote:
    
      
      Hi, 

      

      I loaded the lemna data with bp_seqfeature_load.pl into the
      database and wanted to use bin/prepare-refseqs.pl for the
      reference sequence. But I get:

      

      ------------- EXCEPTION: Bio::Root::Exception -------------

      MSG: unable to find SO or SOFA in the database!

      STACK: Error::throw

      STACK: Bio::Root::Root::throw
      /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368

      STACK: Bio::DB::Das::Chado::sofa_id
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482

      STACK: Bio::DB::Das::Chado::new
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147

      STACK: bin/prepare-refseqs.pl:115

      -----------------------------------------------------------

      Could not open database: 

      ------------- EXCEPTION: Bio::Root::Exception -------------

      MSG: unable to find SO or SOFA in the database!

      STACK: Error::throw

      STACK: Bio::Root::Root::throw
      /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368

      STACK: Bio::DB::Das::Chado::sofa_id
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:482

      STACK: Bio::DB::Das::Chado::new
      /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:147

      STACK: bin/prepare-refseqs.pl:115

      -----------------------------------------------------------

      

      How can that be? I thought if I use Bio-SeqFeature-Store I dont
      need a database like Chado to store the data? Is there somewhere a
      description where I can read more about it and reference
      sequences?

      

      Anja

     		 	   		  

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Mitch S. <mit...@be...>]

  On 09/30/2010 02:25 AM, Anja Friedrich wrote:
> By the way, where did you get the code for the colours in the css file 
> from? Wikipedia is using different ones... and can JBrowse display any 
> colour? As I have to display 12 small motifs I'm running out of colours...

JBrowse (technically, the web browser) can display any color, yes.  
Colors in CSS are hexadecimal numbers; the first third of the digits 
specify the amount of red, the second third specify the amount of green, 
and the last third specify the amount of blue.

So you could specify, say, red with #ff0000, green with #00ff00, and 
blue with #0000ff.  Or, say, a dark red with #550000.  Or whatever you 
wanted.  Most drawing programs will have a tool you can use to choose 
colors, or you could use something like this:

http://www.colorpicker.com/

If you run out of colors, you can also use an image to differentiate 
different motifs; look at the feature, feature2, feature3, feature4, and 
feature5 CSS classes.

Mitch

Re: [Gmod-ajax] error by runing prepare-refseqs.pl

[Anja F. <fri...@ho...>]

Okay, I think I fixed the problem how to specify the reference sequence. But now I get:

Use of uninitialized value in concatenation (.) or string at bin/prepare-refseqs.pl line 113.
Use of uninitialized value $_ in require at (eval 12) line 1.
Null filename used at (eval 12) line 1.

Anja
Date: Thu, 30 Sep 2010 07:49:57 -0700
From: mit...@be...
To: fri...@ho...
CC: gmo...@li...
Subject: Re: [Gmod-ajax] error by runing prepare-refseqs.pl



  


    
  
  
    On 09/30/2010 02:25 AM, Anja Friedrich wrote:
    
      
      By the way, where did you get the code for the colours in the css
      file from? Wikipedia is using different ones... and can JBrowse
      display any colour? As I have to display 12 small motifs I'm
      running out of colours...

    
    

    JBrowse (technically, the web browser) can display any color, yes. 
    Colors in CSS are hexadecimal numbers; the first third of the digits
    specify the amount of red, the second third specify the amount of
    green, and the last third specify the amount of blue.

    

    So you could specify, say, red with #ff0000, green with #00ff00, and
    blue with #0000ff.  Or, say, a dark red with #550000.  Or whatever
    you wanted.  Most drawing programs will have a tool you can use to
    choose colors, or you could use something like this:

    

    http://www.colorpicker.com/

    

    If you run out of colors, you can also use an image to differentiate
    different motifs; look at the feature, feature2, feature3, feature4,
    and feature5 CSS classes.

    

    Mitch