Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-04-08

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All times shown according to UTC.

Time Nick Message
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01:41 spekkio whenever i try the following code http://codepad.org/I7X20Bbh i keep getting the error http://codepad.org/kWbpb9sJ  anyone have any thoughts as to what im doing wrong?
01:53 deafferret spekkio: do you have another ID that works?
01:55 spekkio well i know that id works, cause if i search it on the ncbi site in the nucleotide db it shows the record
01:55 spekkio maybe im using the wrong type of ID with epost
01:55 deafferret ya, I just wanted a different ID -- one that actually works. if you have one handy
01:56 deafferret to see if this is AY331142 specific somehow
01:56 spekkio one sec
01:56 deafferret setting up in my env
01:57 spekkio DQ462159
01:58 spekkio i just pulled up a bunch lemme know if you need more
02:00 deafferret in the perl code I get the same error with DQ462159
02:01 spekkio am i using epost incorrectly, cause i ususally use it with a gi number searching the -protein database, the only thing i switched was -nucleotide as the db, and used an accession number instead of a gi number
02:02 deafferret dunno. trying to debugger the thing to find out  :)
02:02 spekkio kk, thanks so much
02:07 deafferret huh. the remote side only likes numbers, not letters
02:07 deafferret where's the web URL for the thing you're trying to fetch?
02:08 spekkio http://www.ncbi.nlm.nih.gov/nuccore/33090006
02:10 deafferret hmm... need a get_Response example now
02:11 deafferret http://www.bioperl.org/wiki/HOWTO:EUtilities_C​ookbook#Retrieve_raw_data_records_from_GenBank.2C_save_raw_data_to_file.2​C_then_parse_via_Bio::SeqIO perhaps
02:11 spekkio lol im searching the wrong databse
02:11 spekkio change the -nucleotide to -nuccor
02:13 spekkio cause look at the web url
02:13 deafferret how do you see your results?
02:13 spekkio one sec
02:16 spekkio sry i gotta take a phone call then ill post the code for it
02:16 deafferret no worries
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02:40 spekkio k.... its not actually working
02:43 spekkio here is the full code for post/fetch and outputting it to a file
02:43 spekkio http://codepad.org/Sns7GNdp
03:19 deafferret hmm
03:27 deafferret if you     @genbank_na_acc = qw(33090006);    in works fine
03:27 deafferret so apparently you need to hit it with that ID, not AY331142
03:28 deafferret or we're missing some conversion somewhere that's supposed to happen for us
03:28 deafferret spekkio: ^
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03:31 pyrimidine spekkio: epost only allows UIDs
03:32 deafferret pyrimidine: hi! where'd you see that question?
03:32 pyrimidine spekkio: efetch is the only eutil that allows accessions as well as UIDs (i.e. GI)
03:32 pyrimidine from the heavens
03:32 pyrimidine http://irclog.perlgeek.de/bioperl/today
03:32 deafferret impressive
03:33 * deafferret looks around nervously
03:33 deafferret HI INTERNETS!
03:33 pyrimidine was checking backlog to see if I missed anything GSoC-related
03:33 pyrimidine caught this, thought it needed clarifying
03:33 deafferret http://github.com/jhannah/sandbo​x/blob/master/spekkio/efetch.pl
03:34 pyrimidine http://eutils.ncbi.nlm.nih.gov/corehtml/​query/static/efetchseq_help.html#idparam
03:35 pyrimidine http://eutils.ncbi.nlm.nih.gov/corehtml/que​ry/static/epost_help.html#RecordIdentifier
03:36 pyrimidine note that with epost, it says you can use it if WebEnv is used (with that epost, not with the next step)
03:38 pyrimidine okay, gotta go (sleepy time), hope that helps
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13:55 driveby_bot /home/svn-repositories/bioperl: r16949 (dave_messina) : cwd call not used (and can produce error), so I'm removing it.
13:55 driveby_bot Diff: http://tinyurl.com/yly2axk
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17:39 deafferret ...o..  /\
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22:17 deafferret hmm... this appears to not work   http://cpgislands.usc.edu/
22:17 deafferret I think it's trying to stream and image at me... but it's just unicodey jibberish
22:19 deafferret oh. huh. works in IE 8
22:19 deafferret not Firefox
22:19 deafferret No CpG islands found??? Them's fighting words!
22:53 rbuels deafferret: maybe it's not giving a content-type, and IE8 guesses while firefox does not?
22:53 rbuels would not surprise me
22:55 deafferret dastardly!
22:56 rbuels what kind of idiots program a webapp like that
22:56 deafferret other than me?
22:56 rbuels "NOTE Mac users must click refresh"
22:56 rbuels come on now
22:56 deafferret I enjoy websites that offer advice about 6-year-old browser versions
22:57 deafferret nothing more static that browser glitches!

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