[Bioperl-l] looks like a Bio::SeqIO error

[Hilmar Lapp]

Yep, as Chris wrote, there was a bug about the cleanup not being  
complete. Thanks for your report and sticking with it, it helped us  
identify and fix that problem.

	-hilmar

On May 15, 2009, at 4:55 PM, fungazid wrote:

>
> hilmar, I believe your suspicions are wrong. The proof: changing - 
> format to
> 'Fasta' instead of 'largefasta' in:
> Bio::SeqIO->new(-file=> $fileIn, -format => 'Fasta')
> solved my problem (as was suggested, this is probably not the right  
> method
> to use, but it works).
>
>
> Hilmar Lapp wrote:
>>
>> I think you're running up against an OS limit on the number of open
>> files, or the number of files in a directory. You can check (and
>> change) your limits with ulimit.
>>
>> The largefasta modules is designed for reading in and handling large
>> (like, really large - whole-chromosome scale) sequences which, if all
>> held in memory, would exhaust the memory either immediately or pretty
>> quickly. So it stores them in temporary files. Most unix systems will
>> limit the number of files you can have open at any one time.
>>
>> If your sequences in that file aren't huge, largefasta isn't the
>> module you want to use - just use the fasta parser, or if you need
>> random access to sequences in the file (do you?) then Bio::DB::Fasta.
>> Writing sequences to temporary files is a waste of time if they fit
>> into memory just fine.
>>
>> The odd thing is that you actually run up to the limit. Normally the
>> temporary files should be closed and deleted when the sequence  
>> objects
>> go out of scope (I think - should verify in the code of course ...) ,
>> so the fact that they don't lets me suspect that the code snippet  
>> that
>> you presented isn't all that there is to it - are you storing the
>> sequences somewhere in a variable, such as in an array or a hash  
>> table?
>>
>> 	-hilmar
>>
>> On May 15, 2009, at 9:05 AM, fungazid wrote:
>>
>>>
>>> Hello,
>>>
>>> I hope this is the right address for bioperl programming issues.
>>> Bioperl
>>> saves me a lot of time (not to re-invent the wheel), but there are
>>> some
>>> extremely irritating problems (I would change the code myself if I
>>> knew
>>> how).
>>>
>>> I am trying to read a file (~20MB) containing multiple fasta
>>> sequences:
>>>> a
>>> AGTAGTGAGTGCGCTGA.........
>>>> b
>>> GCGCTGAAGTAGTGAGT.......
>>>> c
>>> AGTAGTGAGTGCGCTGA.........
>>>> d...........
>>>
>>> with the following lines:
>>>
>>> my $seqin = Bio::SeqIO->new('-format'=>'largefasta','-file'=> 
>>> $file1);
>>>
>>> LOOP1: while ( my $seqobj1 = $seqin->next_seq())
>>>
>>> {
>>> ......
>>> my $seq=$seqobj1->subseq(1,$seqobj1->length);
>>> .......
>>> }
>>>
>>>
>>> This works right for the first ~30000 contig sequences but then the
>>> following message appears:
>>>
>>> Error in tempdir() using /tmp/XXXXXXXXXX: Could not create directory
>>> /tmp/6eS92VzVjm: Too many links at /usr/share/perl5/Bio/Root/IO.pm
>>> line 744
>>> DESTROY() mysql_insert obj
>>> destroying HANDLE
>>>
>>> What to do ??? (this is only one of some different Bioperl related
>>> bugs that
>>> I'm experiencing)
>>>
>>>
>>>
>>>
>>> -- 
>>> View this message in context:
>>> http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23559474.html
>>> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>>>
>>> _______________________________________________
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>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> -- 
>> ===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
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>>
>
> -- 
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>
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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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