| 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/bioperl-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 patola123hotmail.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/BioPerl-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 |
