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Munirul Islam | 2 Dec 00:44
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on FootPrinter

Hi:

We are trying to install FootPrinter on a linux machine.
But we are getting errors.  We also tried on MAC. Anyone here successfully
installed it?

I saw bioperl supports FootPrinter.
http://search.cpan.org/~birney/bioperl-run-1.4/Bio/Tools/Run/FootPrinter.pm

Your installation experience would definitely help us.

Thank you.
Munir
Computer Science
Wayne State University
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ANJAN PURKAYASTHA | 1 Dec 23:05
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problem with bp_genbank2gff3.pl

hi,
i copied and pasted the genbank2gff3.pls script into a file
/usr/bin/bp_genbank2gff3.pl and tried running it.
error message:
Can't locate object method "FT_SO_map" via package
"Bio::SeqFeature::Tools::TypeMapper" at /usr/bin/bp_genbank2gff3.pl line
285.

any idea how i get to the map FT_SO_map method?
thanks,
anjan

--

-- 
=============================
anjan purkayastha, phd
bioinformatics analyst
whitehead institute for biomedical research
nine cambridge center
cambridge, ma 02142

purkayas [at] wi [dot] mit [dot] edu
703.740.6939
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Scott Cain | 2 Dec 04:14
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Re: problem with bp_genbank2gff3.pl

Hello Anjan,

Did you install BioPerl?  If so, what version?  You shouldn't really
need to copy and paste bp_genbank2gff3.pl; it should just be there.
The error message you got implies that BioPerl isn't installed or
isn't installed correctly.

Scott

On Mon, Dec 1, 2008 at 5:05 PM, ANJAN PURKAYASTHA
<anjan.purkayastha <at> gmail.com> wrote:
> hi,
> i copied and pasted the genbank2gff3.pls script into a file
> /usr/bin/bp_genbank2gff3.pl and tried running it.
> error message:
> Can't locate object method "FT_SO_map" via package
> "Bio::SeqFeature::Tools::TypeMapper" at /usr/bin/bp_genbank2gff3.pl line
> 285.
>
> any idea how i get to the map FT_SO_map method?
> thanks,
> anjan
>
> --
> =============================
> anjan purkayastha, phd
> bioinformatics analyst
> whitehead institute for biomedical research
> nine cambridge center
> cambridge, ma 02142
(Continue reading)

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Heikki Lehvaslaiho | 2 Dec 05:45
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reorgansing tests by group

I just had a go at reorganising some tests by group in bioperl-live.
Seems to work like charm.

The work flow is:

1. mkdir group
2. svn move test.t. group

More instructions are in:

http://www.bioperl.org/wiki/Talk:Release_1.6#Test_suite

The more I think about this the better I like it. By reorganising
tests, we can see what kind of groups were have in Bio name space.
Moving tests around is cheap and easy and does not affect code at all.
We can experiment to our harts content.

Unless I have done some big boo-boo and someone yells at me, I am
going to go on reorganising test (when I've got time later this week).

   -Heikki
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Hilmar Lapp | 2 Dec 06:09
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Re: reorgansing tests by group


On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote:

> The work flow is:
>
> 1. mkdir group

Doesn't that need to be

1. svn mkdir group

or otherwise svn add the directory afterwards?

	-hilmar
--

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================
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neeti somaiya | 2 Dec 06:54
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Problem in OMIM parser

Hi,

I am downloading the OMIM genemap file from here :

ftp://ftp.ncbi.nih.gov/repository/OMIM/

I was using the OMIMparser all these days to parse the genemap and omim.txt
files and get the relevant data, and it was working perfect, but today
suddenly I got an exception at the following line of my code :

 my $omim_parser = Bio::Phenotype::OMIM::OMIMparser->new(-genemap  =>
$genemap,-omimtext => $omimtext);

The exception I got was :

------------- EXCEPTION  -------------
MSG: Gene map file "genemap" is not in the expected format
STACK Bio::Phenotype::OMIM::OMIMparser::_read_genemap
/root/BiologicalDatabases/OMIM/OMIMparser.pm:881
STACK Bio::Phenotype::OMIM::OMIMparser::genemap_file_name
/root/BiologicalDatabases/OMIM/OMIMparser.pm:408
STACK Bio::Phenotype::OMIM::OMIMparser::new
/root/BiologicalDatabases/OMIM/OMIMparser.pm:224
STACK main::main parseOmimData.pl:56
STACK toplevel parseOmimData.pl:39

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

Please suggest what I can do now.
(Continue reading)

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Heikki Lehvaslaiho | 2 Dec 07:05
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Re: reorgansing tests by group

Yes, forgot that! The directory needs to be added to the repository:

1. mkdir group
2. svn add group
3. svn move test1.t. group
4. svn move test2.t. group
5. ...

   -Heikki

2008/12/2 Hilmar Lapp <hlapp <at> gmx.net>:
>
> On Dec 1, 2008, at 11:45 PM, Heikki Lehvaslaiho wrote:
>
>> The work flow is:
>>
>> 1. mkdir group
>
>
> Doesn't that need to be
>
> 1. svn mkdir group
>
> or otherwise svn add the directory afterwards?
>
>        -hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
(Continue reading)

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Chris Fields | 3 Dec 20:53
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Re: reorgansing tests by group


On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote:

> 2008/12/2 Chris Fields <cjfields <at> illinois.edu>:
>> Wow, I go to sleep and the tests are almost reorganized.  Thanks  
>> Heikki!
>>
>> The only (very small) caveat I find to using recursive tests is any
>> additional non-test files we add, including data for tests in the / 
>> data
>> directory, must not end with *.t, otherwise the build file will try  
>> to run
>> it and bomb.  There was one file I changed to .tt which is now  
>> passed over.
>> If needed we can move over to an autogenerated file which  
>> explicitly lists
>> the tests to run (this would likely be at a later point).
>
> Chris,
>
> I'll try to do the rests very soon now. Do not touch the t directory
> until I've committed by reorganisations!

Okay.  I moved Tools already but I'll leave everything else.

>> On a related point, what does everyone think of moving BioPerlTest  
>> to core
>> so the other distributions can use it?  I think it is worth doing
>> eventually, but it could possibly wait until 1.6.x or 1.7.  I have  
>> tested it
(Continue reading)

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Chris Fields | 3 Dec 21:03
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Re: reorgansing tests by group


On Dec 3, 2008, at 12:23 PM, Heikki Lehvaslaiho wrote:

> 2008/12/2 Chris Fields <cjfields <at> illinois.edu>:
>> Wow, I go to sleep and the tests are almost reorganized.  Thanks  
>> Heikki!
>>
>> The only (very small) caveat I find to using recursive tests is any
>> additional non-test files we add, including data for tests in the / 
>> data
>> directory, must not end with *.t, otherwise the build file will try  
>> to run
>> it and bomb.  There was one file I changed to .tt which is now  
>> passed over.
>> If needed we can move over to an autogenerated file which  
>> explicitly lists
>> the tests to run (this would likely be at a later point).
>
> Chris,
>
> I'll try to do the rests very soon now. Do not touch the t directory
> until I've committed by reorganisations!
>
>> On a related point, what does everyone think of moving BioPerlTest  
>> to core
>> so the other distributions can use it?  I think it is worth doing
>> eventually, but it could possibly wait until 1.6.x or 1.7.  I have  
>> tested it
>> out and it works but needs some dependency issues ironed out.
>
(Continue reading)

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Chris Fields | 2 Dec 14:37
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Re: reorgansing tests by group

Wow, I go to sleep and the tests are almost reorganized.  Thanks Heikki!

The only (very small) caveat I find to using recursive tests is any  
additional non-test files we add, including data for tests in the / 
data directory, must not end with *.t, otherwise the build file will  
try to run it and bomb.  There was one file I changed to .tt which is  
now passed over.  If needed we can move over to an autogenerated file  
which explicitly lists the tests to run (this would likely be at a  
later point).

On a related point, what does everyone think of moving BioPerlTest to  
core so the other distributions can use it?  I think it is worth doing  
eventually, but it could possibly wait until 1.6.x or 1.7.  I have  
tested it out and it works but needs some dependency issues ironed out.

chris

On Dec 2, 2008, at 12:05 AM, Heikki Lehvaslaiho wrote:

> Yes, forgot that! The directory needs to be added to the repository:
>
> 1. mkdir group
> 2. svn add group
> 3. svn move test1.t. group
> 4. svn move test2.t. group
> 5. ...
>
>
>   -Heikki
>
(Continue reading)

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Gmane