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Bioperl Generating Error, Please Help To Configure Bioperl!!

Hi I am a novice perl programmer. I just installed bioperl in my mac and when I tried to invoke some programs it generates this king of error. Could you guys please help me understand what is the problem here?? Thanks!!

  Mac:Desktop darwin$ perl bioperl.pl 
    Use of uninitialized value $inFile in string at bioperl.pl line 7.
    Use of uninitialized value $outFile in concatenation (.) or string at bioperl.pl line 8.

    ------------- EXCEPTION: Bio::Root::Exception -------------
    MSG: Could not open >: No such file or directory
    STACK: Error::throw
    STACK: Bio::Root::Root::throw /Library/Perl/5.12/Bio/Root/Root.pm:486
    STACK: Bio::Root::IO::_initialize_io /Library/Perl/5.12/Bio/Root/IO.pm:351
    STACK: Bio::SeqIO::_initialize /Library/Perl/5.12/Bio/SeqIO.pm:491
    STACK: Bio::SeqIO::fasta::_initialize /Library/Perl/5.12/Bio/SeqIO/fasta.pm:87
    STACK: Bio::SeqIO::new /Library/Perl/5.12/Bio/SeqIO.pm:372
    STACK: Bio::SeqIO::new /Library/Perl/5.12/Bio/SeqIO.pm:413
    STACK: bioperl.pl:8
    -----------------------------------------------------------
bioperl
• 5,934 views • link
written by biostar • biostar

how is your code looks like? it seems like an IO error not related to BioPerl, feed your code to the critic - it may explain what is wrong.

• 128 views • link
written by Pavel Senin Pavel Senin

There is no way to answer this without seeing the code in bioperl.pl.

• 241 views • link
written by Neilfws Neilfws

That isn't an installation problem, that stack trace tells you it cannot open a file that it cannot find and compilation warnings for Infile & Outfile. The modules are being loaded properly.

• 183 views • link
written by Vivek Vivek

Thanks Guys!! The problem was that I did not install the cpanm module using sudo -s. It was not root execution, tha's why the error....

• 0 views • link
written by biostar • biostar

No, this is not related to what you posted above. If this were the case you would have seen a compile-time error that said Can't locate Bio/SeqIO.pm in @INC ... and the script would have halted. Clearly, BioPerl is installed because it generated a stack trace. The comments above are correct, the issue is that you are trying to initialize an object with a file that can't be found; that's what the Perl warnings tell you and the BioPerl stack trace below points to the same issue.

• 230 views • link
written by SES SES

1 answer

Thanks, but do I need to keep my perl script in the same lib where I have my .pm files for bioperl or it is going to locate them on its own??

• 0 views • link
written by biostar • biostar

Please update your original post rather than posting other questions as an answer (that makes it easier to see who is participating and what has been solved). The answer to this question is no, and this is not related to your original question.

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written by SES SES

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