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

[Chris Fields]

The problem was that both temp files and temp dirs were created for  
each seq, but only the files were removed (not the dirs).  That's been  
fixed in svn.

Regardless, using 'fasta' format is a better option (though I still  
think using Bio::DB::Fasta is best).

chris

On May 15, 2009, at 3:55 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.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> 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 :
>> ===========================================================
>>
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> -- 
> View this message in context: http://www.nabble.com/looks-like-a-Bio%3A%3ASeqIO-error-tp23559474p23567169.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l