Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-09-28

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All times shown according to UTC.

Time Nick Message
00:05 deafferret huh. bioperl.org table disappears completely when you squish it
00:05 deafferret I hope everyone has wide monitors.
00:06 deafferret oh... nm... it's jumping down the page
00:20 deafferret apparently read-only in Bio/Index/Abstract is a lie...
08:26 faceface ptl: ref?
08:26 faceface (evolutionary psychology)
08:26 faceface had an interesting debate about 'psycogenomics' while at the BGI
08:32 faceface I'll be back... presumably.
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18:08 pyrimidine deafferret: if the Bio/Index/Abstract isn't acting as readonly when set that way, it's a bug (either in the documentation or the implementation).
18:12 deafferret pyrimidine: huh... actually, it appears to be an incompatibility between making an index in an older version of bioperl, then trying to read it with a newer
18:12 deafferret so the issue wasn't read-only, it was that root uses an older bioperl
18:12 pyrimidine ah, the joys of mixing versions...
18:12 deafferret :)  not proven yet
18:13 deafferret I thought it had something to do with the fact that my mega-index is on a network share
18:13 pyrimidine not too surprising if it turns out that way, considering most sysadmins still think 1.4 is the most 'stable'
18:16 deafferret (Bio::Index::Fasta)++ # neat when you need it  :)
18:31 deafferret huh. yup. write with 1.006000 and you can't read with 1.006900
18:31 deafferret at least root is on 1.6  :)
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19:00 pyrimidine The critical thing that changed between the two was how FASTA is parsed in SeqIO
19:02 pyrimidine FASTA is the only seq format that changes $/ (to '\n>' I think), so it removes the initial '>' from all sequences but the first one.
19:03 pyrimidine So, we're now validating for FASTA format based on that first sequence; however, this borked indexing, which has to be adjusted to make sure the first sequence always has a '>'
19:04 pyrimidine (that should read 'Bio::SeqIO::fasta is the only parser that changes', not what I had above)
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