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This queue is for tickets about the Bio-Grep CPAN distribution.

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The Basics
Id: 37910
Status: resolved
Priority: 0/
Queue: Bio-Grep

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Owner: Nobody in particular
Requestors: jamie.duke [...] gmail.com
Cc:
AdminCc:

Bug Information
Severity: Normal
Broken in: 0.10.3
Fixed in: (no value)



Subject: Bug in Bio::Grep::Root.pm
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I am using Bio::Grep v. 0.10.3 on a Windows XP machine with ActiveState Perl v. 5.8.8. I was having issues trying to generate a database. Here is the error message that I was receiving. ------------- EXCEPTION Bio::Root::BadParameter ------------- MSG: Variable looks not valid. STACK Bio::Grep::Root::_check_variable c:/perl/site/lib/Bio/Grep/Root.pm:126 STACK Bio::Grep::Root::is_path c:/perl/site/lib/Bio/Grep/Root.pm:44 STACK Bio::Grep::Backend::BackendI::_copy_fasta_file_and_create_nfo c:/perl/site/lib/Bio/Grep/Backend/BackendI.pm:497 STACK Bio::Grep::Backend::BackendI::_prepare_generate_database c:/perl/site/lib/Bio/Grep/Backend/BackendI.pm:842 STACK Bio::Grep::Backend::Agrep::generate_database c:/perl/site/lib/Bio/Grep/Backend/Agrep.pm:158 STACK toplevel test_agrep.perl.pl:13 ------------------------------------------------------------- Turns out that the absolute path I was trying to use had spaces in it, and the function Bio::Grep::Root::_check_variable with the regex 'path' does not allow for spaces in the filename, which is hard to get around with perl running on Windows not in Cygwin. The fix to this is simple for the next release. Line 109 in Bio::Grep::Root::_check_variable needs to be changed to: "'path' => qr{ ( \A [\w.\-/\\: ]+ \z ) }xms," where there is now a space after the colon to allow spaces in filenames. Thanks!
Thank you very much! It is fixed in 0.10.4.


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