[Bioperl-l] Problem: Can't call method "features" on an undefined value at BIO::DB::GFF.pl
Hang
hangsyin at gmail.com
Mon Jan 21 19:22:55 UTC 2008
Hi, Chris:
Following your suggestion, I added -create flag and the GFF3loader started
to work. Thanks alot!
When I load dmel-all-5.4.gff into mysql with -fast, I had the following
error:
Data too long for column 'attribute_value' at c:/../../../mysql.pm line
510
If I don't use -fast, it is OK, except for the annoying slow speed. Do you
have any suggestion on this?
Best,
Hang
Chris Fields wrote:
>
> It's bp_seqfeature_load.pl (if you have the full bioperl core
> distribution, it's in script/Bio-SeqFeature/Store). I had some
> problems with the fast-loading option but it was likely just my gff
> formatting; example data loaded just fine.
>
> As for the error, you need to use the '-create' flag when initializing
> a database (or wiping data from a current one):
>
> =============================================================
> use Bio::DB::SeqFeature::Store;
> use Bio::DB::SeqFeature::Store::GFF3Loader;
> my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
> -dsn => 'dbi:mysql:test',
> -user => 'root',
> -pass => 'XXXXX',
> -write => 1
> -create => 1);
> my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store =>
> $db,
> -verbose =>
> 1);
> $loader->load(./'dmel-all-r5.4.gff');
> =============================================================
>
> chris
>
> On Jan 20, 2008, at 9:25 AM, Scott Cain wrote:
>
>> Jon,
>>
>> There is a script for loading a SeqFeature database just like the GFF
>> database, though I don't know what it's called off hand (I'm not at my
>> normal computer right now). Be sure to read the documentation and you
>> will probably want to use the 'fast' option (I don't remember what
>> it is
>> called either).
>>
>> Scott
>>
>>
>> ----------------------------------------------------------------------
>> Scott Cain, Ph. D. cain at cshl.edu
>> GMOD Coordinator, http://www.gmod.org/ (216)392-3087
>> ----------------------------------------------------------------------
>>
>>
>> On Sun, 20 Jan 2008, Hang wrote:
>>
>>>
>>> Hi, Scott,
>>> I tried to change sequence-region line to "4 FlyBase
>>> chromosome_arm 1
>>> 1351857 . . . ID=4;Name=4", it doesn't work. "$!" didn't say
>>> anything but
>>> "died at line 12".
>>>
>>> So, I went ahead with the Bio::DB::SeqFeature::Store. Here is my
>>> code to
>>> load the dmel-all-r5.4.gff(from Flybase) to a test database:
>>> =============================================================
>>> use Bio::DB::SeqFeature::Store;
>>> use Bio::DB::SeqFeature::Store::GFF3Loader;
>>> my $db = Bio::DB::SeqFeature::Store->new(-adaptor => 'DBI::mysql',
>>> -dsn => 'dbi:mysql:test',
>>> -user => 'root',
>>> -pass => 'XXXXX',
>>> -write => 1 );
>>> my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store
>>> => $db,
>>> -verbose
>>> => 1);
>>> $loader->load(./'dmel-all-r5.4.gff');
>>> =============================================================
>>> I got bunch of errors like this:
>>> "DBD::mysql::execute failed: Table 'test.locationlist' doesn't
>>> exist at
>>> C:\Biology\perl\site\lib\Bio\DB\SeqFeature\Store\DBI\mysql.pm line
>>> 1316".
>>> The line 1316 in mysql.pm looks like this: $sth->execute($name) or
>>> die
>>> $sth->errstr;
>>> I checked the database test after failed loading. There is only one
>>> table
>>> created, which call 'meta'. I also tried 'grant all on test to
>>> XXX at localhost' and used that -user and -pass to load gff, it didn't
>>> work
>>> either.
>>>
>>> Jon
>>>
>>>
>>> Scott Cain-3 wrote:
>>>>
>>>> Hi Jon,
>>>>
>>>> Well, seeing the error message would be helpful, but my first guess
>>>> without is that there are a few things you can try:
>>>>
>>>> * removing the "sequence-region" line from the GFF file, adding a
>>>> line
>>>> like this:
>>>>
>>>> 4 FlyBase chromosome_arm 1 1351857 . . . ID=4;Name=4
>>>>
>>>> and then reloading the database.
>>>>
>>>> * Or, you may want to consider using Bio::DB::SeqFeature::Store,
>>>> since
>>>> Bio::DB::GFF3 doesn't always behave correctly with complex GFF3
>>>> (that
>>>> is, with three levels of features (like gene, mRNA and CDS)).
>>>>
>>>> Scott
>>>>
>>>> On Sat, 2008-01-19 at 19:49 -0800, Hang wrote:
>>>>> Hi, Scott,
>>>>>
>>>>> After adding die $!, I know something is wrong at line:
>>>>> "my $segment = $db->segment(-name => '4', -start => 20000, -end =>
>>>>> 25000);"
>>>>>
>>>>> my gff file is like this:
>>>>> ##gff-version 3
>>>>> ##sequence-region 4 1 1351857
>>>>> 4 FlyBase transposable_element 2 611 . + .
>>>>> ID=FBti0062890;Name=ninja-Dsim-
>>>>> like
>>>>> {}4829
>>>>> ;Dbxref=FlyBase_Annotation_IDs:TE62890;derived_cyto_location=-;
>>>>> 4 repeatmasker_dummy match 2 347 . + .
>>>>> ID=:1395923_repeatmasker_dummy;Name=1%2C347-AE003845.4-dummy-
>>>>> RepeatMasker;
>>>>> 4 repeatmasker_dummy match_part 2 347 2367 + .
>>>>> ID=:5142029_dummy;Name=:5142029;Parent=:
>>>>> 1395923_repeatmasker_dummy;target_type=so;Target=D83207
>>>>> 5860 6210 +;
>>>>> ...
>>>>> ...
>>>>> I really got confused. Any further suggestion? Thank you!
>>>>>
>>>>> Jon
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Scott Cain-3 wrote:
>>>>>>
>>>>>> Hi Jon,
>>>>>>
>>>>>> I think it's funny that you have "or die" on the database
>>>>>> opening line,
>>>>>> "or die" on the @features line, but you didn't put one on the
>>>>>> $segment
>>>>>> line. Try adding "or die: $!" to the $segment line to see what it
>>>>> says,
>>>>>> also add a 'print $segment' after you create it and before you
>>>>>> try to
>>>>>> get the features from it.
>>>>>>
>>>>>> Clearly, the problem is that $segment is not defined (that is,
>>>>>> nothing
>>>>>> is in it, not that the wrong thing is in it). The next trick is
>>>>>> to
>>>>> find
>>>>>> out why. My first guess, without looking at the data set, is
>>>>>> that the
>>>>>> arm is not really named '4'.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>> On Sat, 2008-01-19 at 10:25 -0800, Hang wrote:
>>>>>>> Hi, everyone,
>>>>>>>
>>>>>>> I met this problem when I was running this script to extract
>>>>>>> features
>>>>>>> overlaps with 4:20,000..25,000. It always responds like "Can't
>>>>>>> call
>>>>>>> method
>>>>>>> "features" on an undefined value at BIO::DB::GFF.pl line XX".
>>>>>>> ==============================================================
>>>>>>> use Bio::DB::GFF;
>>>>>>> use Bio::Tools::GFF;
>>>>>>> my $db = Bio::DB::GFF->new(-adaptor => 'dbi::mysql',
>>>>>>> -dsn =>
>>>>>>> 'dbi:mysql:dmel_gff:localhost',
>>>>>>> -user => 'XXXX',
>>>>>>> -pass => 'XXXX') || die
>>>>> "database
>>>>>>> open failed";
>>>>>>>
>>>>>>> my $segment = $db->segment(-name => '4', -start => 20000, -end =>
>>>>> 25000);
>>>>>>> my @features = $segment->features(-types => ['gene', 'exon',
>>>>>>> 'intron',
>>>>>>> 'five_prime_UTR', 'three_prime_UTR', 'CDS']) or die "no
>>>>>>> features";
>>>>>>> print(scalar(@features)."\n");
>>>>>>>
>>>>>>> ================================================================
>>>>>>> I am using activeperl 5.8.8 and bioperl 1.5.2 under Win32. I
>>>>>>> loaded
>>>>>>> dmel_5.4.gff into mysql database by bulk_load_gff.pl without any
>>>>> error.
>>>>>>> Other methods failed also.
>>>>>>>
>>>>>>> Any help will be deeply appreciated!
>>>>>>>
>>>>>>> Best,
>>>>>>> Jon
>>>>>>>
>>>>>> --
>>>>>>
>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.
>>>>> cain at cshl.edu
>>>>>> GMOD Coordinator (http://www.gmod.org/)
>>>>> 216-392-3087
>>>>>> Cold Spring Harbor Laboratory
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>
>>>>>>
>>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.
>>>> cain at cshl.edu
>>>> GMOD Coordinator (http://www.gmod.org/)
>>>> 216-392-3087
>>>> Cold Spring Harbor Laboratory
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>
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>>
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>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>
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