Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-06-19

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All times shown according to UTC.

Time Nick Message
08:57 faceface joined #bioperl
08:57 faceface hi
08:57 faceface whats a golden path genome?
08:58 faceface "used the human RefSeq gene annotation from golden path December 2001 database to explore further"
08:58 faceface ??
09:01 faceface Draft genome sequence:  The sequence produced by combining the information from individual sequenced clones (by creating merged sequenced contigs and them employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes. (Nickname "golden path".)
09:01 faceface ty
11:04 ptl ?
11:14 faceface ;-)
13:47 ptl just returned from my classes of biostatistics... That makes my head hurt.
13:54 nErVe joined #bioperl
13:54 nErVe hello everyone...
13:55 nErVe i was wondering if there is away i can create random trees by specifying number of leaves
13:57 nErVe any body here.?
14:03 ptl I am here.
14:04 ptl random trees? Yes, I think I've seen that on one of the bioperl methods.
14:04 ptl I think there's a treefactory or something like that
14:09 ptl nErVe: here you are!!! http://doc.bioperl.org/releases/biope​rl-1.5.2/Bio/Tree/RandomFactory.html
14:09 ptl nErVe: exactly what you want, right?
14:10 ptl hahaha, just read a paper where the researchers tell us the orangutan is closer to humans than the chimp... preposterous :)
14:10 ptl funny, indeed.
14:10 ptl hello? nErVe?
14:12 nErVe yeah i got..
14:12 nErVe the thing is im  interested in generating gene tree..
14:12 nErVe i want to test notung
14:12 ptl ?
14:13 nErVe Notung is a tree reconciliation software..
14:13 nErVe which requires both gene tree and species tree
14:13 ptl What is tree reconciliation? Never heard about that.
14:13 ptl Oh... It gets both trees and tries to match then?
14:13 ptl That is rather interesting!
14:14 ptl *both kinds of trees
14:14 nErVe well its takes into account both the gene tree and the species tree and maps duplication events.
14:14 nErVe and loss events..
14:14 ptl Cool.
14:14 nErVe u shld have a look at it.
14:14 nErVe i m currently workin on a similar tool which maps duplication events
14:14 ptl As soon as I finish my master degree, I will. I barely have time to breath now. :(
14:15 nErVe i m a masters student too.
14:15 nErVe where u @
14:15 ptl I work at night (12 AM to 8 AM) then I go to the university. It's very hard to keep up.
14:15 ptl State University of Campinas, Brazil - LGE (http://lge.ibi.unicamp.br)
14:15 nErVe oh where u at.??
14:15 nErVe i mean where u based..
14:15 nErVe I m at the uni of Manchester..?
14:16 ptl Campinas, Brazil - near Sao Paulo...
14:16 nErVe oh cooll..
14:16 ptl Cool... What's your course? Molecular Biology?
14:16 nErVe its Bio-informatics..
14:17 nErVe can i add u as a friend..??
14:17 ptl Sure. Add where? MSN? facebook? orkut?
14:17 nErVe msn messenger
14:17 nErVe wld be gr8..
14:18 nErVe vikram.g@live.in
14:18 nErVe thats my id..
14:18 ptl will add
14:19 ptl (mina is patola123@hotmail.com)
14:19 ptl *mine
14:19 ptl done
14:19 nErVe and ur name..wld be..?
14:19 nErVe Mine is Vikram u can call me VIk
14:22 ptl Cláudio, nicknamed Patola :) Vikram seems an indian name, is that right? I talk to a lot of indian guys where I work.
14:24 ptl Oh, my lunch is ready
14:24 ptl I will leave for a while, bye :)
15:52 alper_ joined #bioperl
16:13 faceface can someone help with a very simple sequence manipulation?
16:14 faceface from nucmer I get...
16:14 faceface [S1]     [E1]  |     [S2]     [E2]  |
16:14 faceface 85738   111331  |   155298   129705  |
16:14 faceface I want to mask that region in teh sequence
16:17 faceface so I open a SeqIO for reading and one for writing, but how do I mask the sequence?
16:22 deafferret mask meaning lower/upper case it?
16:40 faceface mask means Xing it out
16:40 deafferret so ACTGTCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGTTGG  ?
16:41 faceface yo
16:41 rbuels faceface: yough.
16:41 rbuels heh.
16:41 faceface word
16:41 deafferret so substr($seq,85738,30000, "X" x 30000)  ?
16:42 faceface I guess
16:47 faceface how do I write that to an SeqIO?
16:58 faceface ?paste
16:59 faceface why's this broke?
16:59 faceface http://pastebin.com/d7b90d4c1
16:59 faceface apart  from the dumb oneline approach
17:00 faceface there is no output from this script
17:00 faceface I mean, the DQ386163_RX.fasta file is empty
17:00 deafferret only 1 seq per file? or do you need a while() loop?
17:00 faceface no, its a single sequence
17:01 deafferret you'll have to pull out $seq->seq, and substr that and then set seq()
17:01 faceface I mean "yes, it's a single sequence"
17:01 faceface sure, but it should be doing something as is right? If only not much
17:01 deafferret you need a > char in $so file
17:01 faceface maybe the compiler detected that I'm an idiot and does nothing ;-)
17:01 faceface what?
17:02 deafferret -file=>">BacterialGenomes/DQ386163_RX.fasta"
17:02 faceface I thought $seq was an object
17:02 deafferret >
17:02 faceface oh...
17:02 faceface tytyt
17:03 deafferret ya, $seq is an obj. so you need to $seq->seq to get the string
17:03 faceface right
17:03 deafferret then substr that, then  $seq->seq($newseq)
17:03 faceface nofun?
17:04 deafferret :)
17:04 faceface $seq->maskme(x,y)?
17:04 deafferret oh? use that then. didn't know there was one  :)
17:04 deafferret save yourself 3 lines of code  :)  whatever works
17:06 faceface there isn't one
17:06 faceface deafferret: its not the number of lines of code that bothers me, its the average number of bugs that the code will contain ;-)
17:07 deafferret the constant dilemma... write 3 lines of code in 8 minutes, or spend an hour looking for someone else's 3 lines of code that might be better  :)
17:08 deafferret tends to write the apparently-easy stuff himself if not already aware of an available crutch
17:10 faceface spend 10 minutes badgering people who may know where to look ... dilema solved!
17:10 faceface ;-)
17:10 faceface its still crumulant ... http://pastebin.com/d35a5034c
17:10 faceface MSG: Did not provide a valid Bio::PrimarySeqI object
17:11 faceface changed nomenclature a bit from what we had before... $s = object $seq = sequence
17:12 deafferret $so->write_seq($s)     (not $seq)
17:12 faceface I knew that!
17:12 deafferret you might want $seq and $seqstr instead of $s and $seq  :)
17:12 faceface why am I so stupid?
17:12 faceface right
17:13 deafferret or just use $s $ss $sss $ssss $sssss   (joking)
17:13 faceface (serious)
17:13 * deafferret used to work with a guy who always did that
17:13 faceface awesome ;-)
17:13 faceface (if your autistic)
17:14 deafferret his name was Val. All this vars were $v, $vv, $vvv, $v3, $v2 ...   sigh
17:16 faceface bleah! $seq->width dosn't get set by the value used in the input fasta
17:18 faceface does this look like an off by one error to you?
17:18 faceface wc BacterialGenomes/DQ386163*  2221   2227 157610 BacterialGenomes/DQ386163.fasta 2220   2227 157609 BacterialGenomes/DQ386163_RX.fasta
17:19 deafferret I can't find width() anywhere. where do you see that?
17:19 faceface Bio::SeqIO::fasta
17:20 faceface I tried to pass the width of the first sequence object to the second, but it just defaults to 60 in both
17:20 faceface the first object actually has a width of 70
17:20 deafferret show me your code again
17:20 faceface http://search.cpan.org/~cjfields/Bio​Perl-1.6.0/Bio/SeqIO/fasta.pm#width
17:21 faceface problem with using the command line...
17:21 faceface http://pastebin.com/d3bbdeb03
17:21 faceface don't you hate forms that don't have a 'clear' button?
17:22 faceface Don't they know my copy buffer is precious?
17:22 faceface I can guess why it isn't collected from the input file
17:29 rbuels don't do 'new Foo::Bar'.  that syntax is deprecated.
17:29 * rbuels hits faceface with a rolled-up newspaper
17:29 * rbuels also is no help at all
17:30 deafferret faceface: try setting width inside Bio::SeqIO->new() for your $so
17:30 deafferret (maybe it's only used if set at instantiation -shrug-)
17:31 * deafferret doesn't feel like diving that right now
17:31 * faceface leaps out of his slumber
17:31 faceface uh ... ok
17:31 faceface deafferret: yeah, its a lot of mindless work for no real gain
17:36 faceface l8r dudes
17:38 deafferret toodles

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