Camelia, the Perl 6 bug

IRC log for #bioperl, 2009-08-02

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All times shown according to UTC.

Time Nick Message
01:06 Cryonic and what type would that be, ptl?
01:45 kyanardag_ joined #bioperl
01:58 ptl Cryonic: I dunno how to define the type, but I think one can easily auto-recognize as such if one matches the stereotype.
16:04 biomoose joined #bioperl
16:04 biomoose biome: Siddhartha Basu master SHA1-da5028b
16:04 biomoose Added proper superclass
16:04 biomoose http://bit.ly/10Mudq
16:04 biomoose biome: Siddhartha Basu master SHA1-8f9eb0f
16:04 biomoose Added Atomic location
16:05 biomoose http://bit.ly/Lc6X9
16:05 biomoose biome: Siddhartha Basu master SHA1-e04fafb
16:05 biomoose removing unneeded files
16:05 biomoose http://bit.ly/2rukP7
16:05 biomoose biome: Siddhartha Basu master SHA1-c34ff99
16:05 biomoose removed the retired 'Bio' folder
16:05 biomoose http://bit.ly/2yK7s
16:05 biomoose biome: Siddhartha Basu master SHA1-0bf2e0d
16:05 biomoose few comments
16:05 biomoose http://bit.ly/26xaRD
16:05 biomoose biome: Siddhartha Basu master SHA1-ac8c3d6
16:05 biomoose Merge branch 'master' of git@github.com:cybersiddhu/biomoose
16:05 biomoose http://bit.ly/17OWlz
16:05 biomoose biome: Siddhartha Basu master SHA1-c928053
16:05 biomoose Merge branch 'master' of git@github.com:cjfields/biome
16:05 biomoose http://bit.ly/xF0Sy
16:05 biomoose left #bioperl
18:35 hiptobecubic joined #bioperl
18:35 hiptobecubic Does anyone know any tools that can take several sequences and generate the IUPAC consensus?
18:41 hiptobecubic eh.. i guess i'll make one
18:56 ptl the align object has a method for that, isn't it?
18:57 hiptobecubic does it?
18:59 ptl let me check.
19:00 hiptobecubic ptl, i found i think. thakns
19:00 ptl http://doc.bioperl.org/bioperl-l​ive/Bio/Align/AlignI.html#POD23
19:00 ptl yes
19:00 ptl :)
19:00 ptl np
19:01 hiptobecubic ptl, so i make an align obj and call add seq for each seq i want to add
19:02 hiptobecubic The sequences are already aligned, so i should be able to just call consensus_iupac without doing anything else right?
19:03 ptl right
19:03 ptl but you do not need to add_seq
19:03 ptl you can load an alignment straight from disk
19:03 ptl that's what I do usually
19:03 ptl in a .aln or .phy file
19:05 hiptobecubic I just have a directory full of fasta files
19:05 ptl well, in that case you can also go through add_seq...
19:07 hiptobecubic does addseq take a Bio::Seq object or a string of the sequence, it doesn't say
19:07 ptl hm
19:07 ptl lemme check.
19:08 ptl Argument  : a Bio::LocatableSeq object
19:08 ptl order (optional)
19:10 hiptobecubic righto
19:31 hiptobecubic ptl, So regular seq objects are not locatable seq objects.
20:05 Cryonic right, Bio::Seq is not a Bio::LocatableSeq
20:05 Cryonic though they share a lot of methods in common
20:11 hiptobecubic Cryonic, yeah i just manaully made LocatableSeq, set the seq and id and called force_nse
20:45 Cryonic they are nice, unless you are aligning a lot of small sequences to a large one
20:45 Cryonic you can't use the built-in splice method
20:46 Cryonic since you have to pad the seq() with -'s
20:47 Cryonic for me that added up to way too much memory chewed up and lots of compute time wasted putting them into each seq
23:03 hiptobecubic left #bioperl

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