Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-01-12

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All times shown according to UTC.

Time Nick Message
00:09 driveby_bot joined #bioperl
00:09 driveby_bot /home/svn-repositories/bioperl: r16661 (fangly) : Providing explicit Bio::LocatableSeq end() in Bio::Assembly::Tools::Contig​Spectrum::_overlap_alignment
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00:17 driveby_bot /home/svn-repositories/bioperl: r16662 (fangly) : Removed some debugging code
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01:23 driveby_bot /home/svn-repositories/bioperl: r16663 (maj) : adaptor futzes; added TSeq parsing (for fasta rettype) to FetchAdaptor::seq.pm (very much faster than GBSeq parsing)
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01:24 driveby_bot /home/svn-repositories/bioperl: r16664 (maj) : most simple Cookbook recipes tested here; am now official sick of writing tests (but more to come)
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01:25 driveby_bot /home/svn-repositories/bioperl: r16665 (maj) : propset
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01:56 driveby_bot /home/svn-repositories/bioperl: r16666 (kortsch) : POD clean
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01:58 driveby_bot /home/svn-repositories/bioperl: r16667 (maj) : fill out pod for adaptor classes
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02:22 driveby_bot /home/svn-repositories/bioperl: r16668 (maj) : build out pod for fetch adaptors
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03:13 driveby_bot /home/svn-repositories/bioperl: r16669 (maj) : building out the main SoapEU pod
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03:50 driveby_bot /home/svn-repositories/bioperl: r16670 (maj) : main SoapEU pod
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04:59 driveby_bot /home/svn-repositories/bioperl: r16671 (maj) : main SoapEU pod pretty much done
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13:32 space_agent1 I want to write a script that maps the blast output to a reference sequence, like a genome, and displays it graphically. Can anyone point me towards a module I could use for that. In principle it shouldn't be too complicated as the blast output gives kind of coordinates (start stop of Alignment) but practically, you know ;-)
13:38 ende blast output of what?
13:39 ende and what sort of graphical representation are you looking for?
13:51 space_agent1 joined #bioperl
13:51 space_agent1 So like a blastn of a number of pyrosequencing reads against a single longer reference sequence. Graphically I'd like to have an alignment of all the small reads against the longer reference sequence.
13:56 space_agent1 Very similar to the output of the blastn suite here: http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_​TYPE=BlastSearch&PROG_DEF=blastn&BLAS​T_PROG_DEF=megaBlast&BLAST_SPEC=blast2seq.
13:57 space_agent1 But there the number of seqs to be shown in graphical overview is restricted to 1000.
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14:19 space_agent I think for now I'll just use blast 2 sequences until I find a better solution.
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16:37 ende ah gotcha space_agen1
16:37 ende well there are a number of ways you can go about that
16:38 ende are you looking for quick + dirty, or something more persistent ?
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16:43 driveby_bot /home/svn-repositories/bioperl: r16672 (maj) : pod finish
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16:48 driveby_bot /home/svn-repositories/bioperl: r16673 (maj) : DB path for bioperl-run
17:02 deafferret ..@o
17:03 deafferret (that was my dog after she ate my curry this morning)
17:03 deafferret ...  o.   oo@.
17:03 deafferret (that was the phant)
17:05 driveby_bot joined #bioperl
17:05 driveby_bot /home/svn-repositories/bioperl: r16674 (maj) : tag SoapEU port bioperl-dev -> bioperl-run/trunk
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17:06 driveby_bot /home/svn-repositories/bioperl: r16675 (maj) : merge SoapEU to bioperl-run trunk
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17:07 driveby_bot /home/svn-repositories/bioperl: r16676 (maj) : SoapEU tests to bioperl-run trunk
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22:23 driveby_bot /home/svn-repositories/bioperl: r16677 (maj) : remove cruft
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22:24 driveby_bot /home/svn-repositories/bioperl: r16678 (maj) : remove cruft
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22:30 driveby_bot /home/svn-repositories/bioperl: r16679 (maj) : require networking
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23:03 driveby_bot /home/svn-repositories/bioperl: r16680 (maj) : bug squish
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23:05 driveby_bot /home/svn-repositories/bioperl: r16681 (maj) : case
23:14 * deafferret shakes his fist at maj
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