[Bioperl-l] Too many links at LoadHelper.pm

[Scott Cain]

I believe you can call the loading script with more than one GFF file
as the argument, eliminating the need for the for loop.



On Fri, Feb 5, 2010 at 11:25 AM, Fungazid <fungazid at yahoo.com> wrote:
> Scott, Jason, hi,
>
> I replaced my code with:
>
> for(...) {system("bp_seqfeature_load.pl -d contigs -u root -p xxxx ./$file[$i]")==0 or die;}
>
> run it, and it went smoothly (or seem to be like that ).
>
> The reason I used an alternative script is that it is almost identical to bp_seqfeature_load.pl but it calls the following functions only once:
>
> Bio::DB::SeqFeature::Store->new(..)
> Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>
>
> Thanks,
> Avi
>
>
> --- On Fri, 2/5/10, Scott Cain <scott at scottcain.net> wrote:
>
>> From: Scott Cain <scott at scottcain.net>
>> Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm
>> To: "Fungazid" <fungazid at yahoo.com>
>> Cc: Bioperl-l at lists.open-bio.org
>> Date: Friday, February 5, 2010, 5:38 AM
>> Hi Avi,
>>
>> Off hand, I have no idea what is happening.  Is there
>> a reason you
>> aren't using bp_seqfeature_load.pl?
>>
>> Scott
>>
>>
>> On Thu, Feb 4, 2010 at 9:52 PM, Fungazid <fungazid at yahoo.com>
>> wrote:
>> > Bioperl hi,
>> >
>> > I have multiple gff3 files that look like:
>> >
>> >
>> --------------------------------------------------------
>> > ##gff-version 3
>> > # file: temp1.gff3
>> > contig453278    hs    contig    1    699
>>  .    +    .    Name=contig453278
>> > contig453278    hs    alignment    1    194
>>  .    +    .    Name=hs.ENST00000258455
>> > contig453278    hs    alignment    252    699
>>    .    +    .    Name=hs.ENST00000258455
>> > contig453278    hs    mi2    194    252    .
>>    +    .    Name=mi2
>> > contig453278    hs    transcript    104    183
>>    .    +    .
>>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,4
>> > contig453278    hs    transcript    1    9
>>  .    +    .
>>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,1
>> > contig453278    hs    transcript    73    103
>>    .    +    .
>>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,3
>> > contig453278    hs    transcript    10    72
>>    .    +    .
>>  Name=hs.ENST00000258455;ID=transcript-hs.ENST00000258455;Note=CD,2
>> >
>> ---------------------------------------------------------
>> >
>> >
>> >
>> > I uploaded gff3 files to mysql and view the tracks in
>> gBrowse like this:
>> >
>> > --------------------------------------------
>> > Bio::DB::SeqFeature::Store->new(...)
>> >
>> $loader=Bio::DB::SeqFeature::Store::GFF3Loader->new(...)
>> > for($i=0; $i<$#files+1; $i++){
>> > $loader->load($file[$i]);
>> > }
>> > --------------------------------------------
>> >
>> > Eventually after uploading ~15000 small gff3 files I
>> got the error:
>> >
>> > Error in tempdir() using /tmp/XXXXXXXXXX: Could not
>> create directory /tmp/9bbpdE5ibf: Too many links at
>> /usr/local/share/perl/5.8.8/Bio/DB/SeqFeature/Store/LoadHelper.pm
>> line 49
>> >
>> >
>> >
>> > I am trying to see what went wrong, maybe you can
>> rescue me,
>> > Avi
>> >
>> >
>> >
>> >
>> > _______________________________________________
>> > Bioperl-l mailing list
>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.
>>
>>        scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)
>>            216-392-3087
>> Ontario Institute for Cancer Research
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>
>
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research