Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-11-17

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All times shown according to UTC.

Time Nick Message
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04:51 kblin hi folks
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12:17 kai ahrg. $arr1[$i] =~ /[$arr2[$i]]/ is not a comparison if $arr1[$i] is the same as $arr2[$i]
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12:21 kai hm, ok, arguably all the users only ever put single chars in there
12:21 kai but still... yuck
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13:25 dnewkirk_home if you leave the m// empty, it matches to $_, so if $_ is set to your search value, your golden.
13:29 dnewkirk_home $re = qr/$pattern/;
13:30 dnewkirk_home $string =~ /$re/;
13:54 dbolser pyrimidine: the 'model for SNP calling' was changed between version 0.1.7 and 0.1.8 of pileup
13:54 dbolser By default, pileup used the SOAPsnp model for SNP calling. This avoids the floating overflow in the MAQ model which leads to spurious calls in repetitive regions, although these calls will be immediately filtered by varFilter.
13:55 dbolser oh, it should be s/used/uses/
13:55 dbolser .e., 0.1.7 was using maq model and 0.1.8 is using the soapsnp model by default.
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14:09 kai dnewkirk_home: but looking at the users, the author wanted $foo[$i] eq $bar[$i], and only because @foo and @bar contain only single character elements, that happened to work the same
14:13 dnewkirk_home Ahh, I see. I misunderstood. I didn't realize that the goal was to do an equivlency test as opposed to a pattern match.
14:15 kai dnewkirk_home: well, the comment and the code disagreed
14:16 kai that's always fun
14:16 kai so I had a fun time playing "where is this used and what do the callers expect to happen"
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14:44 paulC_ hello
14:44 paulC_ i have a very simple bug fix
14:45 paulC_ is now known as Guest17310
14:45 Guest17310 should I post the bug fix here?
14:46 kai can you put it into a pastebin?
14:47 Guest17310 ok
14:48 kai even better would be to email it to the bioperl-l list
14:50 Guest17310 what is the best way to post it in an email?
14:50 Guest17310 diff?
14:53 kai do you have the fix in git locally?
15:13 Guest17310 kai, I found http://www.bioperl.org/wiki/HOWTO:SubmitPatch and I'm trying to follow it now
15:14 kai uhm, that's not really up-to-date
15:15 kai http://www.bioperl.org/wiki/Using_Git might be better
15:16 kai if you have the patch in git, git format-patch -1 should dump the last commit in your repository as a text file in your current directory in a form that's useable
15:18 Guest17310 kai, I'm a bit confused
15:19 Guest17310 hold a sec, i'm trying to figure something out
15:19 kai if you can provide more information on what you're confused about, maybe I can help
15:20 Guest17310 464c464 <     foreach (qw(display_id accession_number primary_id desc id length)) { --- >     foreach (qw(display_id accession_number primary_id desc id)) {
15:20 Guest17310 this is a "diff" of the changed file (Bio::Seq::PrimaryQual.pm) to the original file.
15:20 Guest17310 All I did was to add "length" to the foreach loop
15:21 Guest17310 when I used git format-patch -1 , the resulting file didn't contain anything that I changed
15:21 Guest17310 so I'm not sure what git format-patch -1 does
15:21 kai did you commit your changes?
15:21 Guest17310 do I even have commit access?
15:22 kai you have on your local checkout
15:22 kai that's what distributed version control systems are all about :)
15:22 Guest17310 i thought I had to register or something
15:22 Guest17310 so I can change anything and commit it? seems odd to trust a newbie like me
15:23 Guest17310 are the commits checked by somebody before they become final?
15:23 kai well, you can commit to your local repository, not to the official one :)
15:23 Guest17310 i thought so
15:23 kai see http://www.spheredev.org/wiki/Git_for_the_lazy
15:23 Guest17310 so after I commit to my local, then what do I do?
15:24 kai then you do the format-patch call
15:24 Guest17310 oh ok
15:25 Guest17310 lemme do some reading and try to figure this out
15:25 Guest17310 thanks for your help
15:30 Guest17310 kai, on a different topic...
15:30 Guest17310 why isn't there a seq() subroutine in Bio/Seq/PrimaryQual?
15:31 Guest17310 seems like there should
15:31 Guest17310 instead the module has a "to_string()" subroutine
15:46 Guest17310 kai, what do I do with the output file from "git format-patch -1"? Should I send it to bioperl-l list?
15:46 kai yeah
15:48 kai Bio::Seq::PrimaryQual doen't implement Bio::SeqI
15:49 kai not sure if that's on purpose
15:50 kai but as far as I see Bio::Seq::PrimaryQual doesn't contain a sequence in any case
15:57 Guest17310 i don't know all the design implications but I'd argue that it is a sequence of numbers
15:58 Guest17310 i discovered this problem because I have a script that reads fasta formatted files and uses seq->seq() to output the sequences....
15:58 Guest17310 then I switched to using a quality (.qual) file and I thought it would just work and that "seq->seq()" would output the sequence of numbers
16:08 kai no idea about the design decisions either, but I'd argue that most of my colleagues would not think of numbers if I say "sequence"
16:08 kai :)
16:25 Guest17310 but then why is it in a module prefixed with "Bio::Seq"
16:25 Guest17310 too misleading then
16:27 Guest17310 I guess I could I write my own Bio::Seq::PrimaryQual->seq() subroutine and post it on bioperl-l
17:55 pyrimidine Guest17310: There is a bit of redundancy with the Bio::Seq stuff.  Some of those should probably go into a Qual namespace, but since they were originally added to Bio::Seq::* that's where they stuck
17:55 pyrimidine Guest17310: there is code in Bio::Seq that is actually Bio::PrimarySeqI and not Bio::SeqI as well
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18:36 deafferret ooOOoo.. ...
18:37 perl_splut wonderful landscape there
18:46 deafferret Poop Mountain.
19:12 * rbuels inhales the crisp mountain air
19:22 perl_splut right time of year for crisp mountain air
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