Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-10-22

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All times shown according to UTC.

Time Nick Message
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00:06 rbuels well stop putting bugs in there then, of course!
00:07 rbuels pshaw
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04:47 k2b joined #bioperl
04:47 k2b hi
04:48 k2b hello
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13:01 deafferret dnewkirk: hire a goon to break your kneecaps if you don't fix in in 3 hours
13:01 deafferret invigorating!
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21:34 artisofficial joined #bioperl
21:35 artisofficial i have a n00b question, how can i read a csv file through the bioperl modules?
21:35 perl_splut depends
21:36 perl_splut csv isn't a really well defined format
21:36 artisofficial i want to (1) read a csv then (2) parse the file via the comma delimiters
21:36 artisofficial i am not sure if bioperl does this already
21:37 perl_splut I don't believe that it does
21:37 artisofficial ah okay
21:37 perl_splut since it isn't a defined format
21:38 artisofficial in order to pipe my program, i would need to read a csv, otherwise it reads .fa files perfectly
21:38 perl_splut well, then you can create a CSV module for SeqIO to use that is specific to your format
21:39 perl_splut such as assuming that the Sequence is always the last item in each line
21:39 artisofficial can the delimiters for SearchIO be changed from gaps to commas?
21:40 perl_splut the delimiters are set by the specific sub-module that is being used
21:40 perl_splut next_* functions can be defined in sub-modules causing them to change the behavior of the function
21:42 perl_splut when you call Bio::SearchIO->new(-format=>'xxx'); The -format flag is telling SearchIO which sub-module to use when parsing the file
21:42 artisofficial thanks! that directs me to a couple of place i can look :)
21:42 perl_splut though I think you want SeqIO and not SearchIO
21:42 artisofficial my program uses SearchIO, mainly
21:42 perl_splut guessing you're parsing things like Blast reports then
21:43 artisofficial yes, then piping the results through a series of filter scripts
21:43 artisofficial which is why i would like to be able to intrepret csv files
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