| Time |
S |
Nick |
Message |
| 00:35 |
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kyanardag_ joined #bioperl |
| 02:13 |
|
CIA-60 |
bioperl-live: Robert Buels topic/longest_orf * ra60b745 / (Bio/PrimarySeqI.pm t/Seq/PrimarySeq.t): refactored ORF finding in Bio::PrimarySeqI, in order to add capability of finding a sequence's longest ORF. tests not quite passing - http://bit.ly/d8YLgn |
| 02:28 |
|
deafferret |
not I, sorry |
| 02:34 |
|
deafferret |
hmm... /me tries rbuels' fancy gitk toy |
| 02:35 |
|
deafferret |
in an attempt to understand this fangly situation |
| 02:56 |
|
deafferret |
GitX++ |
| 03:01 |
|
deafferret |
oh, ha! the r in front of git revisions should be removed from the IRC bot :) re71c10c looks awfully like it starts with r :) |
| 03:06 |
|
deafferret |
git is fun. it makes me feel really stupid constantly :) |
| 03:10 |
|
deafferret |
my branch Jul 2009 -> this week looks pretty cool in GitX. Then especially how I merged it twice at the end |
| 03:10 |
|
deafferret |
cluelessness++ |
| 03:32 |
|
CIA-60 |
bioperl-live: Jay Hannah master * r3198b27 / Changes : Simplifying further since there was no response to my BUGS question on the mailing list. - http://bit.ly/dtN2t5 |
| 04:21 |
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| 04:36 |
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| 06:41 |
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| 09:01 |
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kd` joined #bioperl |
| 09:01 |
|
kd` |
hello |
| 09:02 |
|
kd` |
could someone announce the perl survey to the bioperl mailing list please. The official announcement is here: http://news.perlfoundation.org/ |
| 09:02 |
|
kd` |
oops, here: http://news.perlfoundation.org[…]erl-survey-1.html |
| 12:14 |
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| 12:14 |
|
kblin |
hi folks |
| 12:18 |
|
kblin |
I'm trying to parse HMMer3 hmmscan results using Bio::SearchIO and the parser reads in the data without throwing an error, but it fails to find any classification hits. |
| 12:47 |
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| 13:02 |
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| 14:38 |
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| 15:12 |
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| 15:40 |
|
spekki01 |
anyone that's used hmmer3 to search a sequence db know how to make it give some output to the terminal so you can tell its actually searching? |
| 15:53 |
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| 16:05 |
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| 17:26 |
|
deafferret |
spekki01: so currently you have no output at all, but 100% CPU use? |
| 17:27 |
|
rbuels |
spekki01: well you can tail its output files |
| 17:27 |
|
rbuels |
spekki01: tail -f <output file> |
| 17:27 |
|
rbuels |
spekki01: you can see what it's writing, if anything |
| 17:35 |
|
spekki01 |
well i think it was hanging and not doing anything |
| 17:35 |
|
spekki01 |
and yeah it was 100% usage |
| 17:35 |
|
spekki01 |
heres what i think is wrong |
| 17:36 |
|
spekki01 |
the file i got from NCBI was ther protein database nr.gz, after dl and unpacking. i look into it and it has weird end of line character all ther "^A" and i think hammer doenst recognice these and is trying to read the whole 6gig file as one line... |
| 17:37 |
|
spekki01 |
so im attempting to write a quick shell command using awk or sed to change all of the ^A to \n |
| 17:39 |
|
deafferret |
perl -p -i -e 's/\cA/\n/g' filename ? |
| 17:41 |
|
spekki01 |
i was gonna do sed '/s/^A/\n/g' test.txt but its not working |
| 17:41 |
|
spekki01 |
lemme try what you have |
| 17:41 |
|
deafferret |
^A is "line begins with an A" |
| 17:42 |
|
spekki01 |
oh |
| 17:42 |
|
deafferret |
unless you're actually hitting Control-L Control-A there |
| 17:42 |
|
spekki01 |
ok yours works way better |
| 17:43 |
|
deafferret |
hmm, not control-L... apparently I've forgotten the key sequence in bash... ignore that part :) |
| 18:06 |
|
spekki01 |
deafferret: how would i change that script so instead of \n i wanted a space instead would it be somethign like perl -p -i -e 's/\cA/ /g' filename? |
| 18:08 |
|
deafferret |
yup |
| 18:08 |
|
deafferret |
perldoc perlrun |
| 18:08 |
|
spekki01 |
kk tx |
| 18:08 |
|
deafferret |
you probably want to start doing -i.bak or something |
| 18:08 |
|
deafferret |
so it's not overwriting your file, it creates a new file |
| 18:08 |
|
deafferret |
since you're not sure you're doing it right :) |
| 18:09 |
|
spekki01 |
yeah i have copies lol i dont need to spend another 2 hours dling the file |
| 18:09 |
|
deafferret |
:) |
| 18:10 |
|
deafferret |
i usually proof-of concept against head -1000 files |
| 18:31 |
|
spekki01 |
k well im back to running my hmmer searches on my newly fixed protein db, but i still cant tell if it searching or just hanging. I did tail -f outputfile and it shows nothing, is there anyway to have hmmsearch do some kind of verbose output so i know it at least not just stuck on something? |
| 18:31 |
|
spekki01 |
i went through the manual and i just ont see any options that output something to the terminal |
| 18:41 |
|
deafferret |
strace should dump an infinite amount of garbage to your screen as it runs... |
| 18:43 |
|
deafferret |
as far as anything useful goes, if the man page doesn't say anything you're probably stuck |
| 18:44 |
|
deafferret |
if your same command works on smaller datasets, and your big set isn't running the system out of memory, then it'll probably finish eventually |
| 18:44 |
|
deafferret |
but if the authors didn't hook it for "0.02% complete" output then I don't know how you'll know |
| 18:45 |
|
deafferret |
hmms are a fad. just stall and no one will want the results :) |
| 18:45 |
|
deafferret |
like dna analysis :) |
| 18:46 |
|
spekki01 |
lol |
| 18:46 |
|
deafferret |
next week someone will discover a molecule more interesting than dna, then we'll all jump on that new bandwagon |
| 18:46 |
|
spekki01 |
well the command worked on a smaller database so im assuming its running |
| 18:47 |
|
deafferret |
your database is just 1 massive file? or lots of files? |
| 18:47 |
|
spekki01 |
the only difference between the databases was the larger one had all these ^A 's in it but i replaced those with spaces so it's in the same format as the smaller one |
| 18:47 |
|
spekki01 |
one massive 6gig file |
| 18:48 |
|
deafferret |
re: ^A: scary |
| 18:49 |
|
spekki01 |
what does that ^A mean anyway is it a space character on a different system or something? |
| 18:49 |
|
deafferret |
no clue |
| 18:53 |
|
spekki01 |
i feel bad for running this search its eating up all the cpu |
| 18:53 |
|
dnewkirk |
you can use the --cpu paramter to specify the number of cores to use |
| 18:54 |
|
deafferret |
spekki01: leave me 1 cpu please |
| 18:54 |
|
spekki01 |
lol |
| 18:55 |
|
spekki01 |
i might have to set that, its been running 70 min on the servers and using all the cpu |
| 18:55 |
|
dnewkirk |
leave him the pentium II |
| 19:02 |
|
* dnewkirk |
realizes he has an odd sense of humor. decides to stop foisting it on the channel |
| 19:07 |
|
spekki01 |
omfg did you see the google logo today lol |
| 19:07 |
|
spekki01 |
playable pacman :) |
| 19:15 |
|
deafferret |
lol cool |
| 19:15 |
|
deafferret |
beat level 1, hit a bug -- went right through a ghost somehow |
| 19:15 |
|
deafferret |
:) |
| 19:16 |
|
* deafferret |
goes back to work |
| 19:24 |
|
spekki01 |
sigh running 2 hours 7 min and still nothing from my hmmer search, can it really take this long when going through a really big db file? |
| 19:26 |
|
deafferret |
yup. |
| 19:27 |
|
deafferret |
computers should generally be avoided |
| 19:27 |
|
spekki01 |
maybe i should just go home and let it run over the weekend |
| 19:27 |
|
* deafferret |
passes the bottle to spekki01 |
| 19:27 |
|
spekki01 |
lol |
| 19:27 |
|
deafferret |
shh... I won't tell rbuels |
| 19:39 |
|
|
splut joined #bioperl |
| 20:30 |
|
kblin |
evening folks |
| 20:31 |
|
spekki01 |
hi |
| 20:31 |
|
* deafferret |
waves |
| 20:34 |
|
kblin |
I'm trying to parse HMMer3 hmmscan results using Bio::SearchIO. the parser reads in the data without throwing an error, but it fails to find any classification hits |
| 20:34 |
|
kblin |
is there any trick to it, or is the new format just not supported? |
| 20:35 |
|
deafferret |
kblin: is the data you're trying to find in BioPerl definately in your results file? |
| 20:37 |
|
kblin |
deafferret: yeah, I get results all right |
| 20:37 |
|
kblin |
so loading the file works |
| 20:38 |
|
deafferret |
no, I mean are your "classification hits" definately part of the results files? just bioperl isn't parsing them (apparently) |
| 20:39 |
|
deafferret |
can you nopaste your code somewhere so we can see what you're trying to do? |
| 20:39 |
|
kblin |
sure |
| 20:41 |
|
kblin |
http://codepad.org/5rfWJ7AE |
| 20:42 |
|
deafferret |
have a small result file snippet so I can see what your "classification hits" are? |
| 20:42 |
|
kblin |
and the start of the hmmer results file looks like http://codepad.org/9FKP7I06 |
| 20:42 |
|
deafferret |
:) |
| 20:43 |
|
deafferret |
I don't see 'class*' in that result file |
| 20:43 |
|
deafferret |
c-Evalue ? |
| 20:45 |
|
* deafferret |
sighs mightily in the general direction of $vendor in San Diego |
| 20:49 |
|
kblin |
hm |
| 20:50 |
|
kblin |
there should be a class* in the result file? |
| 20:53 |
|
kblin |
ah, I see it in the hmmerpfam results of an old run :) |
| 20:56 |
|
deafferret |
so the bioperl parser can't find it 'cause it's not there? :) |
| 20:58 |
|
kblin |
ok, so basically the bioperl parser doesn't support hmmer3 yet.. :) |
| 21:01 |
|
deafferret |
i don't know squat about hmmer formats, so I don't know. I'm happy to help you debug it if you give me the info I need to reproduce your results |
| 21:02 |
|
kblin |
I can dump a full result file somewhere, if that helps |
| 21:03 |
|
deafferret |
well, I don't yet understand what you're expecting to parse that isn't parsing |
| 21:04 |
|
deafferret |
all you've said is 'classification hits', but I have no idea what you mean by that |
| 21:04 |
|
deafferret |
where, in the result file(s), are these items you want to parse? |
| 21:04 |
|
kblin |
ah |
| 21:05 |
|
kblin |
basically I'm expecting the contents of the "Scores for complete sequence (score includes all domains): |
| 21:05 |
|
kblin |
" |
| 21:05 |
|
kblin |
table to show up in the results object |
| 21:05 |
|
kblin |
that's what happens when I parse the hmmer2 output |
| 21:06 |
|
CIA-95 |
bioperl-live: Chris Fields master * rcbed980 / Bio/Tools/EUtilities/Link.pm : small doc fix, more to come - http://bit.ly/cy4DNQ |
| 21:06 |
|
deafferret |
so you're saying bioperl appears to be ignoring lines 11-21? |
| 21:07 |
|
kblin |
yeah |
| 21:07 |
|
kblin |
the old file format looks like http://codepad.org/yMBVAP86 |
| 21:08 |
|
deafferret |
huh. ok, lemme give this a stab |
| 21:08 |
|
* deafferret |
clocks out |
| 21:10 |
|
deafferret |
what's the stands filename extension for these? |
| 21:10 |
|
deafferret |
.hmmsearch ? or...? |
| 21:11 |
|
kblin |
out framework names them .hsp, but I don't know if that's the accepted standard |
| 21:13 |
|
kblin |
ok, so the way I read Bio/SearchIO/hmmer.pm line 301, this looks like a check for the new output format |
| 21:13 |
|
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pyrimidine joined #bioperl |
| 21:15 |
|
* rbuels |
waves at pyrimidine |
| 21:15 |
|
* pyrimidine |
waves back |
| 21:16 |
|
CIA-95 |
bioperl-live: Lincoln Stein lstein-seqfeature-store-summaries * r974abf3 / (8 files in 4 dirs): gene coverage stats seem to be working,,,basically - http://bit.ly/dezhO3 |
| 21:17 |
|
pyrimidine |
lincoln knows github |
| 21:17 |
|
rbuels |
and football, and baseball ..... |
| 21:18 |
|
* rbuels |
dates himself |
| 21:18 |
|
deafferret |
wow. deafferret thought about, then passed on that joke |
| 21:18 |
|
rbuels |
deafferret: *you*? *passed*? on a joke? |
| 21:19 |
|
rbuels |
i'm shocked. shocked! |
| 21:19 |
|
deafferret |
purl: rbuels is also below the bottom of deafferret's joke barrel |
| 21:19 |
|
deafferret |
barell? |
| 21:19 |
|
deafferret |
barrell? |
| 21:19 |
|
deafferret |
bear-ul |
| 21:20 |
|
rbuels |
i always spelled it barayl |
| 21:20 |
|
deafferret |
all wood gnomes do |
| 21:20 |
|
rbuels |
dunno, i could be wrong |
| 21:21 |
|
deafferret |
ogres tend toward bear-ul |
| 21:21 |
|
kblin |
deafferret: so, the output of the Dumper call for the file I pasted dumps http://codepad.org/SDSG6yCU |
| 21:21 |
|
* rbuels |
has no idea what deafferret is talking about |
| 21:22 |
|
deafferret |
rbuels: oh, sorry. forgot you were in the wood gnome closet |
| 21:23 |
|
deafferret |
"The server at github.com is taking too long to respond." |
| 21:23 |
|
deafferret |
maybe we should host our own SVN server or something? |
| 21:23 |
|
rbuels |
lol |
| 21:23 |
|
deafferret |
kblin: I'm seeing the same thing. someday you will be able to see my code here http://github.com/jhannah/sand[…]tree/master/kblin |
| 21:24 |
|
deafferret |
kblin: so next I was going to try to find that top block somehow |
| 21:24 |
|
deafferret |
probably perl -d inside hmmer.pm or something |
| 21:25 |
|
deafferret |
github.com/bioperl had a good run, but maybe it's time we gave the strategy a 2nd think |
| 21:25 |
|
* deafferret |
runs and hides |
| 21:25 |
|
kblin |
deafferret: I'm expecting http://codepad.org/QMX0xIF8 (cut a little) |
| 21:25 |
|
deafferret |
github being down is funny for the first 60s or so. then... not so much |
| 21:26 |
|
* deafferret |
wells up a little |
| 21:26 |
|
deafferret |
kblin: k. hmm |
| 21:29 |
|
deafferret |
looks like hmmer.pm hasn't been touches since 2008. hmmer_pull since 2006 |
| 21:30 |
|
deafferret |
how old is this hmmer3 format? |
| 21:30 |
|
kblin |
hm, hmmer3 has been released in 2009, but has been in development for a couple of years |
| 21:32 |
|
kblin |
but I agree the fact that there's no "implement hmmer3 support" is a bit suspicious |
| 21:32 |
|
kblin |
nasty that the new format seems close enough to the old hmmsearch format for the parser to not throw an error |
| 21:33 |
|
deafferret |
if (/^Scores for complete sequences/o) { |
| 21:33 |
|
deafferret |
has an extra 's' on the end :/ |
| 21:34 |
|
kblin |
ah, durn |
| 21:35 |
|
kblin |
ok, so both hmmer3 and hmmer2 have a hmmsearch binary |
| 21:35 |
|
kblin |
the manual claims the hmmscan output (that's what I'm trying to parse) is the same as the hmmsearch output |
| 21:35 |
|
kblin |
but probably that only holds in hmmer3 |
| 21:36 |
|
kblin |
and it seems like that subtly changed from the hmmer2 hmmsearch output |
| 21:36 |
|
kblin |
so I misread the docs |
| 21:36 |
|
deafferret |
$self->{'_reporttype'} never gets set, so we're never going to hit the block of your interest...? |
| 21:37 |
|
kblin |
hm, where's that actually coming from? :) |
| 21:37 |
|
kblin |
I mean I know that parser works for the old format :) |
| 21:38 |
|
deafferret |
end_element() sets it |
| 21:40 |
|
kblin |
ah |
| 21:40 |
|
kblin |
I take uc $1 uppercases $1? :) |
| 21:41 |
|
deafferret |
ya |
| 21:42 |
|
kblin |
ok. looks like I'll be spending some fun time writing a parser for hmmscan data myself then |
| 21:42 |
|
kblin |
or rather, see if I can fiddle this into hmmer.pm |
| 21:42 |
|
deafferret |
kblin: well, please fix bioperl :) |
| 21:42 |
|
deafferret |
add lots of tests |
| 21:43 |
|
deafferret |
write a new hmmer.pm and we'll throw the old one out, assuming yours does everything |
| 21:43 |
|
|
rdesfo joined #bioperl |
| 21:43 |
|
pyrimidine |
there was someone working on a hmmer3 set f parsers on the list |
| 21:43 |
|
deafferret |
or write hmmer3.pm, which would be better than bioperl having nothing |
| 21:43 |
|
pyrimidine |
might be worth asking about it there |
| 21:44 |
|
pyrimidine |
I'll see if I can dig up who it was... |
| 21:44 |
|
* deafferret |
races pyrimidine |
| 21:45 |
|
kblin |
pyrimidine: yeah, I susbcribed to the list earlier today, but my university likes to use graylisting, so the confirmation email always takes a while |
| 21:45 |
|
pyrimidine |
Thomas Sharpton |
| 21:45 |
|
kblin |
http://bioperl.org/pipermail/b[…]ruary/029259.html <-tbat one? |
| 21:46 |
|
pyrimidine |
no |
| 21:46 |
|
rdesfo |
hello, I'm going into bioengineering and I was wondering if there where any projects I could participate in regarding bioperl? |
| 21:46 |
|
deafferret |
http://article.gmane.org/gmane[…]1880/match=hmmer3 ? |
| 21:46 |
|
kblin |
http://bioperl.org/pipermail/b[…]ruary/032338.html |
| 21:46 |
|
kblin |
got it |
| 21:47 |
|
rbuels |
pyrimidine: i am emailing the search.cpan.org maints about that POD rendering thing |
| 21:47 |
|
rbuels |
pyrimidine: i will CC bioperl-l |
| 21:47 |
|
pyrimidine |
kblin: http://lists.open-bio.org/pipe[…]0-May/031172.html |
| 21:47 |
|
pyrimidine |
though, looking at that repo, there is nothing |
| 21:48 |
|
deafferret |
shouldn't bioperl-dev stuff just be a branch in bioperl-live instead? |
| 21:48 |
|
pyrimidine |
it should |
| 21:49 |
|
kblin |
pyrimidine: that certainly _looks_ nice :) |
| 21:50 |
|
kblin |
I'll email the author and ask, thanks |
| 21:50 |
|
rbuels |
deafferret: yes. |
| 21:50 |
|
spekki01 |
when using the nice command anyone know the default nice value that say a shell script would run at? i know its off topic. |
| 21:50 |
|
deafferret |
rdesfo: there's gobs of bioperl bugs. wade in! :) |
| 21:51 |
|
deafferret |
rdesfo: github.com/bioperl |
| 21:51 |
|
deafferret |
rdesfo: bioperl.org |
| 21:51 |
|
rdesfo |
thanks I've been to bioperl.org |
| 21:51 |
|
deafferret |
rdesfo: and/or do some of my work for me. I have ~80 tickets you could work |
| 21:51 |
|
rdesfo |
:) |
| 21:51 |
|
rbuels |
spekki01: i think it's 0 |
| 21:51 |
|
rbuels |
spekki01: on most systems ... |
| 21:51 |
|
deafferret |
i'll go 80/20 on my stipend with ya |
| 21:51 |
|
rbuels |
spekki01: #perl would be a better place to ask |
| 21:52 |
|
deafferret |
:) |
| 21:52 |
|
rbuels |
spekki01: same server as this channel |
| 21:52 |
|
deafferret |
rdesfo: biodoc.ist.unomaha.edu/rt guest guest |
| 21:52 |
|
spekki01 |
ok |
| 21:53 |
|
deafferret |
kblin: let us know what Tom says. I don't see his code in bioperl-dev |
| 21:54 |
|
deafferret |
kblin: i usually say what pyrimidine says. it just takes me 15X longer :) |
| 21:54 |
|
rdesfo |
deafferret: thanks |
| 21:56 |
|
deafferret |
pyrimidine: where is this code? http://lists.open-bio.org/pipe[…]0-May/031172.html |
| 21:57 |
|
kblin |
thanks for the help folks |
| 21:58 |
|
kblin |
SIGWIFE, though, be back tomorrow :) |
| 21:58 |
|
deafferret |
heh. welcome to the scramble! hope you can help :) |
| 21:58 |
|
deafferret |
ERUNLIKEHELL |
| 21:59 |
|
pyrimidine |
deafferret: it isn't there |
| 21:59 |
|
deafferret |
r16984 |
| 21:59 |
|
deafferret |
created a dir, which was later deleted? |
| 21:59 |
|
pyrimidine |
svn ls svn+ssh://dev.open-bio.org/home/svn-repositories/bioperl/bioperl-hmmer3 |
| 21:59 |
|
pyrimidine |
gets nothing |
| 22:00 |
|
pyrimidine |
the svn repo is still there, just read-only |
| 22:00 |
|
deafferret |
huh. ok. thanks. /me clocks back in |
| 22:02 |
|
rbuels |
pyrimidine: http://search.cpan.org/~cjfiel[…]SeqI.pm#translate versus http://search.cpan.org/~cjfiel[…]SeqI.pm#translate |
| 22:02 |
|
rbuels |
pyrimidine: i think this is actually what is causing brian's problem |
| 22:03 |
|
rbuels |
pyrimidine: the former (which does not include lots of the POD on translate()) shows up first in the search.cpan.org results |
| 22:03 |
|
rbuels |
pyrimidine: which is probably why Brian clicked on it |
| 22:03 |
|
rbuels |
pyrimidine: is there a dev release or something that should be deleted? |
| 22:04 |
|
* pyrimidine |
looking |
| 22:05 |
|
pyrimidine |
I wonder if that was something that occurred during the POD cleaning. |
| 22:05 |
|
pyrimidine |
had a POD checker run through the code at one point, which reported back bad spots |
| 22:05 |
|
pyrimidine |
I fixed those |
| 22:05 |
|
pyrimidine |
but maybe broke something?!? |
| 22:05 |
|
pyrimidine |
rbuels: dev release? |
| 22:06 |
|
rbuels |
pyrimidine: if you do a CPAN search for 'Bio::PrimarySeqI' you get a top hit that has [Developers] next to it |
| 22:06 |
|
rbuels |
i'm not sure what that is |
| 22:06 |
|
rbuels |
just guessing that it might have something to do with a dev release |
| 22:06 |
|
rbuels |
or maybe it doesn't |
| 22:08 |
|
pyrimidine |
I could delete those |
| 22:09 |
|
pyrimidine |
odd, looking at those, not seeing the dev versions for bioperl core |
| 22:10 |
|
pyrimidine |
Oh, I see what you mean |
| 22:11 |
|
pyrimidine |
it's showing upp in the name |
| 22:11 |
|
pyrimidine |
*up |
| 22:11 |
|
pyrimidine |
Bio::PrimarySeqI [Developers] - Interface definition for a Bio::PrimarySeq |
| 22:11 |
|
rbuels |
pyrimidine: yes, in the search hit |
| 22:12 |
|
pyrimidine |
SeqI as well, but not all interfaces |
| 22:12 |
|
pyrimidine |
Bio::Align::AlignI doesn't |
| 22:12 |
|
rbuels |
pyrimidine: any idea where the erroneous one came from? |
| 22:13 |
|
* rbuels |
writes a followup on the search.cpan.org rt ticket |
| 22:13 |
|
pyrimidine |
Not sure; SeqI has it right in the POD |
| 22:13 |
|
rbuels |
well, in the source that is being linked from those pages |
| 22:14 |
|
rbuels |
seems to me, there are probably some wires crossed in the html generation or the versions of the packages that are uploaded, or both |
| 22:14 |
|
pyrimidine |
PrimarySeqI doesn't though (for 1.6.1) |
| 22:14 |
|
pyrimidine |
or 1.6.0 |
| 22:15 |
|
pyrimidine |
almost seems like a caching issue |
| 22:15 |
|
rbuels |
pyrimidine: examples/root/lib ? |
| 22:15 |
|
rbuels |
pyrimidine: does that ring a bell? |
| 22:15 |
|
rbuels |
notice one has that in the page |
| 22:15 |
|
rbuels |
er, in the path |
| 22:16 |
|
pyrimidine |
yes, that's supposed to be an example file |
| 22:16 |
|
rbuels |
um. |
| 22:16 |
|
rbuels |
http://cpansearch.perl.org/src[…]io/PrimarySeqI.pm |
| 22:16 |
|
rbuels |
there is an old version of PrimarySeqI included in the dist. |
| 22:16 |
|
pyrimidine |
ok, that probably explains it, then |
| 22:16 |
|
rbuels |
and search.cpan.org is indexing it |
| 22:16 |
|
pyrimidine |
right |
| 22:16 |
|
rbuels |
and it's the top hit! |
| 22:17 |
|
deafferret |
! |
| 22:17 |
|
pyrimidine |
yes, that's one oddity of the indexing there |
| 22:17 |
|
rbuels |
depth-first maybe |
| 22:17 |
|
pyrimidine |
the other is it will find the first module with BioPerl in the name and use that as the description of the repo |
| 22:17 |
|
rbuels |
o_O |
| 22:18 |
|
pyrimidine |
hence the reason we have BioPerl.pm |
| 22:18 |
|
pyrimidine |
in the root dir |
| 22:18 |
|
rbuels |
ah. |
| 22:18 |
|
pyrimidine |
So, if you look up BioPerl, it will find that |
| 22:19 |
|
pyrimidine |
'Perl Modules for Biology' |
| 22:19 |
|
pyrimidine |
instead of |
| 22:19 |
|
pyrimidine |
'Loader for LiveSeq from EMBL entries with BioPerl' |
| 22:19 |
|
pyrimidine |
which comes from Bio::LiveSeq::IO::BioPerl |
| 22:19 |
|
pyrimidine |
okay, gotta run |
| 22:19 |
|
pyrimidine |
o/ |
| 22:19 |
|
deafferret |
o7 |
| 22:20 |
|
deafferret |
sudo rbuels /nick rbuels____ # so conversations line up correctly |
| 22:22 |
|
rbuels |
pyrimidine: do those modules in examples need to be there? |
| 22:22 |
|
rbuels |
pyrimidine: can we just delete them and re-upload a new dist? |
| 22:22 |
|
rbuels |
pyrimidine: ok, i'm going to close the RT ticket then |
| 22:24 |
|
rbuels |
sudo deafferret get a better irc client |
| 22:25 |
|
deafferret |
tsk tsk. not a team player, that one. |
