Re: [Gusdev-gusdev] LoadPfam compile error

[Deborah F. P. <pi...@pc...>]

Hi Chetna,

This isn't actually an answer to your question but an alternative plugin.  
For the dotsbuild, we use a more generic plugin to load pfam sequences, as
well as other sequences, into GUS,
GUS::Common::Plugin::InsertNewExternalSequences. 


Here's the bit of the pipeline that does it, you can pick out the command 
line pretty easily. It was used recently but you should always check the 
regex as they are prone to change:

 #>gnl|Pfam|pfam00291 PALP, Pyridoxal-phosphate dependent enzyme
    $regex_src_id = "^\\>\\w+\\|\\w+\\|\\w+\\s(pfam\\w+)";
    $regex_name = "^\\S+\\spfam\\w+\\,\\s([\\w\\_\\s]+)\\,\\s";
    $regex_desc = "^\\S+\\spfam\\w+\\,\\s(.*)";
    
    my $pfamArgs = "--verbose --table_name 'DoTS::MotifAASequence' 
--sequencefile '$downloadSubDir/PFAM' --external_database_release_id 
$pfamDB --regex_source_id \"$regex_src_id\" --regex_name \"$regex_name\"  
--regex_desc \"$regex_desc\"";
    
    $mgr->runPlugin("insertPfam", 
"GUS::Common::Plugin::InsertNewExternalSequences", $pfamArgs,
		   "Inserting Pfam", 'downloadGOStuff');


                                                                     
Debbie

                                                        



On Thu, 22 May 
2003,
Chetna Warade wrote:

> Hi all,
> 
> I am getting a compiler error for LoadPfam.pm
> Heres a snapshot:
> 
> [chetna@mango chetna]$ ga
> GUS::Common::Plugin::LoadPfam
> Reading properties from
> /home/gus_home/config/GUS-PluginMgr.prop
> 
> ERROR: Can't use bareword ("getArgs") as a HASH ref
> while "strict refs" in use at
> /home/gus_home/lib/perl/GUS/Common/Plugin/LoadPfam.pm
> line 125.
> Compilation failed in require at (eval 1) line 1.
> 
> 
> --------------------------- STACK TRACE
> -------------------------
>        
> GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'Can\'t use bareword ("getArgs") as a HASH ref while
> "strict refs...') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 249
>        
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 362
>        
> GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 284
>        
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'GUS::Common::Plugin::LoadPfam') called at
> /home/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
> line 193
>        
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x80fbb0c)',
> 'ARRAY(0x8105184)') called at /home/gus_home/bin/ga
> line 11
> [chetna@mango chetna]$
> 
> Look forward to chain of emails!,
> Chetna
> 
> 
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