[Bioperl-l] question temp files in blast

dimitark at bii.a-star.edu.sg dimitark at bii.a-star.edu.sg
Wed Dec 11 01:53:52 UTC 2013

Hi guys,
i have a question about StandAloneBlastPlus and File::Temp.

I encountered a problem which arises from File::Temp in my particular  
script. In previous email i said i forced StandAloneBLastPLus to  
accept a TEMP_DIR which i give through modifying BlastMethods.pm and  
StandAloneBlastPlus.pm. This works but not always and that is because  
File::Temp is using the built in perl function rand() which uses  

Now in brief: my script is splitting a large FASTA into smaller ones  
and for each of the smaller ones is starting a new thread of BLAST  
with as many threads as desired. Also is creating a special TEMP_DIR  
for each thread in which the temp blast files are stored: file.fas and  
the blast_result. However because of the rand() some clashing of file  
names occurs because there is not enough randomness and some of my  
threads die, not always but very often.

So my question is the following. Should i try to modify  
BlastMethods.pm and StandAloneBlastPlus.pm further so that i can  
manually specify the file names of the temp files or to use another  
module like  Math::Random::Secure in order to produce a really random  
number which i can then pass to srand() after i create my threads so  
that there is no temp file names clashing?

The easiest is to just use additional module but then more  
dependencies just for one random number. On the other hand if i modify  
the current modules i will be sure that there wont be a chance to have  
temp file name clashing at all and no further dependencies.

I am sorry if my email seems too messy but i tried to put it really brief.

Any advice is welcomed!

Thank you for your time


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