Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-19

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All times shown according to UTC.

Time Nick Message
03:49 driley joined #bioperl
17:34 faceface hi
17:35 faceface given two aligned sequences (in a non-standard format), how do I create an alignment object and write out some standard format?
17:35 * faceface is reading http://www.techfak.uni-bielefeld.de/​bcd/Perl/Bio/UnivAln-1.009/UnivAln.p​m.html#Object_Creation_in_a_Nutshell
17:36 faceface Bio::AlignIO ?
17:37 faceface Bio::Align::AlignI
17:40 faceface Bio::SimpleAlign
17:45 faceface how do I slurp? I know that is like day 1 of perl...
17:46 faceface ust set the built in variable $/ (the input record separator) to the undefined value and read in the file with <>:
17:49 rbuels faceface: Bio::SimpleAlign is an alignment object
17:49 rbuels faceface: it's what the AlignIO parsers mostly are creating as output
19:18 balin if AlignIO does not know the format, then you can just read in the sequences manually and then add them both to an empty alignment with add_seq(). After that they can be printed out in any format using AlignIO
20:28 vein joined #bioperl
22:26 ryanjyoder joined #bioperl
22:30 ryanjyoder hello, Ive been trying to figure this out for a while now, but with little luck.  Are there any interface changes from 1.4 to 1.6? if so where can I find what they are? i basically want to know what could break if I upgrade.
23:38 ryanjyoder left #bioperl

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