Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-05-23

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All times shown according to UTC.

Time Nick Message
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16:27 prostem hi guys i have a problem with running a perl script that uses Bio::Seq
16:28 prostem can some one please help me decipher it?
16:30 prostem it says alphabet not ok for bio::seq=HASH(0x3dc87d8)
16:31 prostem it essential runs my script and doesnot complete it and gives me this message along with generating partial output
16:31 rbuels prostem: paste the script and the whole output to http://gist.github.com
17:04 prostem hello guys i have uploaded my program and input files to gist
17:05 prostem https://gist.github.com/987060
17:05 prostem hope someone can help
17:09 rbuels prostem: ok, put in the error message you are seeing also
17:09 rbuels prostem: (including the command you're using to invoke it)
17:14 prostem hello rbuels, i just edited the gist and included the error code and also the commands i used
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18:25 rbuels prostem: sorry, had to go to a meeting
18:25 * rbuels looks
18:27 rbuels prostem: you probably need to pass '-alphabet' => 'rna'  to your Bio::SeqIO invocations
18:28 rbuels prostem: i bet what's going on is that SeqStats needs to know the alphabet to calculate stats
18:29 rbuels prostem: and maybe the sequences that you're getting in from the Bio::SeqIO objects don't have their alphabets set
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21:48 * jhannah lools
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