[GUSDEV] ISF testing

[<hen...@gm...>]

Hi,

Trying to test ISF plugin. This is the output I received....

[juca@desterrensis Plugin]$ ga
GUS::Supported::Plugin::InsertSequenceFeatures --mapfile
/home/juca/GUS-Files/ISF/genbank2gus.xml --seqFile
/home/juca/GUS-Files/ISF/Z_mobilis.fasta --fileFormat genbank
--extDbName 'TESTE' --extDbRlsVer '2005-09-06' --soCvsVersion 1.42
Fri Sep 23 17:10:01 2005        ARGS    algoinvo        1
Fri Sep 23 17:10:01 2005        ARGS    comment
Fri Sep 23 17:10:01 2005        ARGS    commit  0
Fri Sep 23 17:10:01 2005        ARGS    debug   0
Fri Sep 23 17:10:01 2005        ARGS    defaultOrganism
Fri Sep 23 17:10:01 2005        ARGS    description
Fri Sep 23 17:10:01 2005        ARGS    downloadURL
Fri Sep 23 17:10:01 2005        ARGS    extDbName       TESTE
Fri Sep 23 17:10:01 2005        ARGS    extDbRlsDate
Fri Sep 23 17:10:01 2005        ARGS    extDbRlsVer     2005-09-06
Fri Sep 23 17:10:01 2005        ARGS    failDir
Fri Sep 23 17:10:01 2005        ARGS    fileFormat      genbank
Fri Sep 23 17:10:01 2005        ARGS    filename
Fri Sep 23 17:10:01 2005        ARGS    gff2GroupTag    GenePrediction  Gen=
e
Fri Sep 23 17:10:01 2005        ARGS    gffFormat       2
Fri Sep 23 17:10:01 2005        ARGS    group
Fri Sep 23 17:10:01 2005        ARGS    gusconfigfile =20
/usr/local/GUS/gus.properties
Fri Sep 23 17:10:01 2005        ARGS    help
Fri Sep 23 17:10:01 2005        ARGS    helpHTML
Fri Sep 23 17:10:01 2005        ARGS    isUpdateMode    0
Fri Sep 23 17:10:01 2005        ARGS    mapFile
/home/juca/GUS-Files/ISF/genbank2gus.xml
Fri Sep 23 17:10:01 2005        ARGS    naSequenceSubclass
Fri Sep 23 17:10:01 2005        ARGS    project
Fri Sep 23 17:10:01 2005        ARGS    projectName
Fri Sep 23 17:10:01 2005        ARGS    restartPoint
Fri Sep 23 17:10:01 2005        ARGS    seqFile
/home/juca/GUS-Files/ISF/Z_mobilis.fasta
Fri Sep 23 17:10:01 2005        ARGS    seqIdColumn     source_id
Fri Sep 23 17:10:01 2005        ARGS    seqSoTerm
Fri Sep 23 17:10:01 2005        ARGS    seqType
Fri Sep 23 17:10:01 2005        ARGS    soCvsVersion    1.42
Fri Sep 23 17:10:01 2005        ARGS    sqlVerbose      0
Fri Sep 23 17:10:01 2005        ARGS    testNumber
Fri Sep 23 17:10:01 2005        ARGS    user
Fri Sep 23 17:10:01 2005        ARGS    verbose 0
Fri Sep 23 17:10:01 2005        ARGS    veryVerbose     0
Fri Sep 23 17:10:01 2005        COMMIT  commit off
Fri Sep 23 17:10:01 2005        ALGINVID        104

ERROR:
Cannot import or construct new object for qualifier handler class
'GUS::Supported::SpecialCaseQualifierHandlers'
Can't modify constant item in scalar assignment at (eval 24) line 1, near "=
))"
Bareword "GUS::Supported::Plugin::InsertSequenceFeatures" not allowed
while "strict subs" in use at (eval 24)  line 1.

STACK TRACE:
 at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperSet.pm
line 73        GUS::Supported::BioperlFeatMapperSet::_parseMapFile('GUS::Su=
pported::BioperlFeatMapperSet=3DHASH(0x9486
68c)', '/home/juca/GUS-Files/ISF/genbank2gus.xml',
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a2 4160)')
called at /usr/local/GUS/gus_home/lib/perl/GUS/Supported/BioperlFeatMapperS=
et.pm
line 17        GUS::Supported::BioperlFeatMapperSet::new('GUS::Supported::B=
ioperlFeatMapperSet',
'/home/juca/GUS-Fil es/ISF/genbank2gus.xml',
'GUS::Supported::Plugin::InsertSequenceFeatures=3DHASH(0x8a24160)')
called at /usr/loc
al/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm
line 335      =20
GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin=
::InsertSequenceFeatures=3DH
ASH(0x8a24160)', 'HASH(0x9486608)') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.p m line
469
eval {...} called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line
461        GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::Pl=
uginMgr::GusApplication=3DHASH(0x84d7c2
0)', 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at
/usr/local/GUS/gus_home/lib/perl/GUS/Plug inMgr/GusApplication.pm line
380        GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr:=
:GusApplication=3DHASH(0x84d7c20)',
'GU S::Supported::Plugin::InsertSequenceFeatures') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusAp plication.pm line
288        GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::Gus=
Application=3DHASH(0x84d7c20)',
'GUS::S upported::Plugin::InsertSequenceFeatures') called at
/usr/local/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplic ation.pm line
197        GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::Gus=
Application=3DHASH(0x84d7c20)',
'ARRAY( 0x84eb568)') called at /usr/local/GUS/gus_home/bin/ga line 11


Hope it helps debugging...



Henrique Cesar Lemos Juc=E1 - http://www.bioinformatica.ufsc.br

"As soon as you concern yourself with the "good" and "bad" of your fellows,
you create an opening in your heart for maliciousness to enter. Testing,
competing with, and criticizing others weaken and defeat you."

Morihei Ueshiba, O-Sensei (1883-1969)