Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-02-01

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All times shown according to UTC.

Time Nick Message
05:07 readwrite joined #bioperl
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08:07 perl_splut left #bioperl
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10:06 gawbul hmmm
10:06 gawbul MSG: Each line of the fasta entry must be the same length except the last.
10:06 gawbul Line above #3 'AGGCAAAAAGGATGAAATTC..' is 61 != 79 chars.
10:06 gawbul I'm getting that from a script, that has worked fine until now
10:07 gawbul I've checked the sequence and all lines are the same!
10:07 gawbul length that is
10:07 gawbul What could that be?
10:08 gawbul hmm, for some reason it's comparing it with the header line?
10:10 gawbul ah, i think it's because there is a space between the > and the identifier
10:13 gawbul when building a sequence object using Bio::Seq->new, do you have to specify the primary_id or display_id, because that is the only thing I changed!
10:13 gawbul ??
10:16 gawbul is that a bug? perhaps it should throw an error if they aren't given... or ensure that the desc line doesn't have a space preceding it if there is no primary_id/display_id given!?
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12:27 kai gawbul: a space at that position seems to be invalid FASTA, though I'm not sure if there's an official spec
12:27 gawbul yeah
12:27 gawbul but i was using Bio::Seq->new to build the sequence objects
12:28 gawbul so I wonder if that was a bug?
12:28 gawbul It works fine if I give the primary_id/display_id, but if ommit those then it failed when i was parsing using Bio::DB::FASTA
12:28 kai sounds like it
12:29 gawbul I'll submit a bug then
14:09 kai thanks :)
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17:25 * deafferret waves
17:32 * rbuels blurbles
17:54 * deafferret lools
17:55 deafferret rbuels: yapc this year?
17:58 rbuels hmmm
17:59 * rbuels looks at the sit
17:59 rbuels e
18:43 * deafferret demands yapc += rbuels
18:57 perl_splut yapc == 0
19:06 deafferret perl_splut: false!
19:06 * deafferret cries a little
19:22 perl_splut you tried to do a some with a string which caused perl to evaluate it as a 0
19:22 perl_splut :)
19:22 perl_splut yapc .=" rbuels"
19:31 rbuels i am actually a constant.
19:33 deafferret oh? your attendence has been variable over the last 2 years
19:33 deafferret tsk tsk
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