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

[Mark A. Jensen]

That's a good thought; when writing a Bioperl
tempfile, I find I must

($fh, $fn) = tempfile();
$fh->close;
$seqio = Bio::SeqIO( -file => ">$fn", -format=>'fasta');

since the better way (always using the filehandle)

($fh, $fn) = tempfile;
$seqio = Bio::SeqIO( -fh => $fh, -format=>'fasta');

doesn't seem to work, though $fh should be open
for both writing and reading. If people do the former
kludge without closing the handle, File::Temp can't
auto-unlink, but it won't cluck about it either.

If I missing something about writing to temp filehandles
here, please set me straight-
cheers MAJ
----- Original Message ----- 
From: "Florent Angly" <florent.angly at gmail.com>
To: "Chris Fields" <cjfields at illinois.edu>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Friday, February 05, 2010 10:24 PM
Subject: Re: [Bioperl-l] Too many links at LoadHelper.pm


> It can't be, Chris, because I use the workaround mentioned here: 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2577#c5
>
> It seems like temporary files keep accumulating assembly after assembly. 
> Looking at the lsof command, I get a lot of files described as "(deleted)". I 
> am thinking that maybe some filehandle is not closed or something.
>
> I'll investigate...
>
> Florent
>
> On 06/02/10 13:13, Chris Fields wrote:
>> Florent,
>>
>> The Bio::Assembly error is documented in Bugzilla:
>>
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2577
>>
>> Switching to a Bio::SeqFeature::CollectionI capable of distinguishing 
>> features by seq_id (such as Bio::DB::SeqFeature::Store) may be the best way 
>> to go.
>>
>> chris
>>
>> On Feb 5, 2010, at 9:06 PM, Florent Angly wrote:
>>
>>
>>> I've run into this issue very recently, albeit working on something 
>>> unrelated to loading GFF files: generating many small independent 
>>> assemblies. Maybe there's a bug in the tempdir() code, or its documentation 
>>> is not clear. I will take a look at it when I have some time.
>>> Florent
>>>
>>>
>>> On 05/02/10 22:27, Mark A. Jensen wrote:
>>>
>>>> The tempfiles are not being unlinked before there are too many for the OS 
>>>> to handle.
>>>> Sounds like this may be your job, fungazid, if you're not employing the 
>>>> script (but
>>>> not sure about that)
>>>> ----- Original Message ----- From: "Fungazid"<fungazid at yahoo.com>
>>>> To:<Bioperl-l at lists.open-bio.org>
>>>> Sent: Thursday, February 04, 2010 9:52 PM
>>>> Subject: [Bioperl-l] Too many links at LoadHelper.pm
>>>>
>>>>
>>>>
>>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>>
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>>
>
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