Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-02-28

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All times shown according to UTC.

Time Nick Message
00:59 CIA-66 bioperl-live: Florent Angly master * r4ecdb18 / (Bio/DB/Query/HIVQuery.pm t/RemoteDB/HIV/HIVQuery.t): Fixed bug for fields without aliases in HIVQuery - http://git.io/PmLFIw
00:59 CIA-66 bioperl-live: Florent Angly master * r2bc6058 / Bio/PopGen/IO/phase.pm : Fixed bug in PopGen: sorting values lexically instead of numerically when unsure that values will be numerical - http://git.io/CYOgcw
01:10 CIA-66 bioperl-live: Florent Angly master * r65261c6 / (Bio/SeqIO/embl.pm t/SeqIO/embl.t): Fixed some undefined warnings in SeqIO::embl - http://git.io/_vU2cw
01:26 CIA-66 bioperl-live: Florent Angly master * rc2eecf4 / t/SeqIO/fastq.t : Fixed wrong lives_and test syntax in fastq test - http://git.io/fT3k2Q
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03:48 Zapanese please help
03:49 Zapanese I got this error msg "End tag mismatch (Hsp != Hsp_hit-frame)[Ln: 276, Col: 83595756]"
03:51 Zapanese (Now I got XML file from NCBI BLAST site and tried to use BLAST parser)
03:52 audy Zapanese: context?
03:53 Zapanese thank you reply!context?code..?
03:56 Zapanese I got 2 BLAST XML files;first file is fine.2nd is something wrong,but I can't understand why these two files differ..
03:57 Zapanese I'm sorry my poor English and can't understand (bio)perl very much..
04:07 Zapanese I looked at line 276 of XML file.However, I couldn't find anything wrong;Hsp tag was closed and matched.
04:07 audy Zapanese: see http://bioperl.org/wiki/IRC#Getting_help. Post the file and code (if you can) to gist.github.com
04:09 Zapanese thank you
04:11 Zapanese code:https://gist.github.com/84b44b941472b432115b
04:13 Zapanese I want to add my XML file,but I'm sorry I can't..I got XML file from NCBI Protein BLAST,and I copied sorce file ,pasted to txt editor, and created .xml file.
04:13 Zapanese (very bad English I wrote..X(
04:15 Zapanese I use this code to parse BLAST.xml
04:17 Zapanese I have two XML file from ncbi.I use this code for one and got good output file.
04:19 Zapanese however other is something wrong..
04:52 CIA-66 bioperl-live: Florent Angly master * rd587561 / (Bio/Assembly/IO/sam.pm t/Assembly/IO/sam.t): __PACKAGE__ is not interpolated inside quotes - http://git.io/7Iajrw
04:52 CIA-66 bioperl-live: Florent Angly master * r7ba2e1a / (Bio/Assembly/IO/bowtie.pm t/Assembly/IO/bowtie.t): Bowtie tests needs Bio::DB::Sam (+extratab cleaning) - http://git.io/riPnhA
04:57 CIA-66 bioperl-live: Florent Angly master * r68c9d58 / Build.PL : Recommend Bio::DB::Sam and IO::Uncompress::Gunzip in Build.PL - http://git.io/QEm0nw
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17:16 scottcain does anybody have an opinion about #!/usr/bin/env perl versus #!/usr/bin/perl?  Are there any gotchas associated with using env?
17:19 audy scottcain: I've never had a problem with it. I guess the only gotcha would be env not being there
17:20 scottcain audy: thanks, though I have no idea how likely it is that env not be there.
17:21 scottcain it feels like it's always there for any moderately modern operating system.
17:21 scottcain (I gave up supporting Windows some time ago :-)
17:22 audy I have no idea how that stuff works on Windows.
17:22 audy #!C:\progra~1\perl\perl.exe ??
17:23 scottcain Typically, I see "#!perl" on windows machines
17:23 audy does windows have ENV variables or do you have to use the registry?
17:23 scottcain beats me; that's why I gave it up :-)
17:24 audy I'm teaching python for premeds and half the class is using windows. I feel so sorry for them
17:24 scottcain Sounds fun ;-)
17:26 scottcain (though I'm pretty sure windows does have environment variables, but I don't know if there is anything like /usr/bin/env on windows)
17:26 * scottcain doubts it.
17:38 rbuels scottcain: /usr/bin/env perl is the usual.
17:38 rbuels scottcain: it works on most things.
17:39 rbuels dunno about windows though
17:40 scottcain rbuels: yep, that's what I thought.  I've got lots of scripts to update.
17:45 CIA-66 bioperl-live: Brian Osborne master * r65fb72f / Bio/Tree/TreeFunctionsI.pm : Remove Node from 'use base', it's unnecessary - http://git.io/j_7Z2Q
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18:37 CIA-66 biome: Chris Fields topic/from_string * r86bdb9c / (lib/Biome/Location/Simple.pm lib/Biome/SeqFeature/Generic.pm): more cleanup - http://git.io/eqrFKQ
18:37 CIA-66 biome: Chris Fields topic/from_string * rcd6dd14 / lib/Biome/Role/Location/Locatable.pm : fix thinko; locations can have an undefined start/end - http://git.io/iuW6UA
18:37 CIA-66 biome: Chris Fields topic/from_string * r4c782b8 / lib/Biome/Role/Location/Collection.pm : remove writer (not used) - http://git.io/2f-kog
18:37 CIA-66 biome: Chris Fields topic/from_string * r3e471cf / (lib/Biome/Location/Simple.pm lib/Biome/SeqFeature/Generic.pm): clean up a little; may remove start/end flipping completely (GIGO) - http://git.io/nsIshQ
18:37 CIA-66 biome: Chris Fields topic/from_string * r3e840f8 / lib/Biome/Role/Location/Simple.pm : more clean up; simplify the methods, deal with undef start/end (though a little kludgy) - http://git.io/2OhuYw
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19:26 CIA-66 biome: Chris Fields topic/from_string * r760ae39 / lib/Biome/Role/Location/Simple.pm : remove comment - http://git.io/8URj8A
19:27 pyrimidine mwahaha
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20:16 CIA-66 biome: Chris Fields master * r760ae39 / lib/Biome/Role/Location/Simple.pm : remove comment (+9 more commits...) - http://git.io/8URj8A
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