Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-06-11

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All times shown according to UTC.

Time Nick Message
00:01 deafferret fooled you! added
00:01 deafferret would be nice to be able to link to more info somewhere though... his Gsoc blog?
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00:20 pyrimidine deafferret: the blog would be good, yes
00:21 pyrimidine huh, there's the CIA bot
00:23 deafferret CIA-94: wiki yourself
00:24 * pyrimidine wishes i could live on Skullcrusher Mountain
00:27 diconzine deafferret perl cant handle with lines 'out of order'?
00:28 deafferret diconzine: I don't know what that is.  in any event, lets talk in #R or #perl-help. this is definately not bioperl  :)
00:29 diconzine ok
00:50 pyrimidine diconzine: sounds like you want something like Tie::File, maybe?
00:53 diconzine i think it is, but i thought perl would be able to handle lines in a way i wouldnt need to read it sequentially every time.. i mean.. 'oh i'm writing line 70 at the moment but i want to change a value in line 32 and put it to the line before mine
00:56 deafferret R solution:  http://github.com/jhannah/sa​ndbox/tree/master/diconzine
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01:10 pyrimidine diconzine: Tie::File can do that very easily.  It's just a tied array.
01:10 pyrimidine tie @array, 'Tie::File', filename or die ...;
01:10 pyrimidine push @array, new recs...;
01:10 pyrimidine @old_recs = splice @array, 3, 7, new recs...;
01:10 pyrimidine pretty nice
01:11 pyrimidine indices are line nums; $array[13] = 'blah';
01:11 diconzine hmmmm
01:11 pyrimidine seems to be what you want, correct?
01:12 diconzine both yours and deafferret's are good :o
01:12 diconzine i think i will try both
01:12 diconzine @_@
01:13 pyrimidine nice, github now has gitref: http://gitref.org/
01:13 diconzine pyrimidine but can i write in that file refered in $array[i]?
01:13 pyrimidine yes
01:14 pyrimidine $array[13] = 'blah'; # replaces that line with 'blah'
01:14 diconzine oh
01:14 diconzine but how i select a field from this line
01:14 diconzine i mean
01:14 diconzine field 7 with tab separator?
01:15 diconzine need to make the split again?
01:15 pyrimidine are you just trying to get one column of data?
01:15 pyrimidine or column/row?
01:15 diconzine hm
01:16 diconzine something like that:
01:16 diconzine i open an input file and start reading it with foreach line
01:17 diconzine and open an output file for writing
01:17 diconzine i repeat the $line[1] of the input
01:18 diconzine then i go to line2
01:19 pyrimidine and what do you on line 2?
01:20 diconzine check if field 7 in the line before is bigger than the field 3 in the actual line
01:20 diconzine if it is
01:20 pyrimidine magic happens?
01:20 diconzine make the value of the field 7 of that line equals to field 3 - 1
01:20 pyrimidine ok
01:20 diconzine lol
01:21 diconzine then the rest is the same
01:21 pyrimidine so, it seems like iteration through the file is required.  deafferret's option, using R, is probably best
01:21 diconzine hm
01:21 diconzine i think so
01:21 diconzine R seemed very simples to deal with
01:22 diconzine *simple
01:22 pyrimidine yes
01:22 pyrimidine you would just pull the entire table into memory, then process the table, then output the table
01:22 diconzine pyrimidine if there are many tables and gff stuffs in bioinformatics
01:22 diconzine why perl is the 'chosen' language
01:22 diconzine ?
01:22 pyrimidine text processing
01:22 pyrimidine try doing that in R
01:23 diconzine hm
01:23 diconzine but text processing is so important in bioinfo?
01:23 pyrimidine R is not made for text processing, just like perl is not made for statistical analysis
01:23 diconzine i'm new in the area
01:23 diconzine hm
01:23 pyrimidine yes, it is a very good skill to have
01:24 pyrimidine no matter what lang you use
01:24 pyrimidine perl, ruby, python, etc.
01:24 pyrimidine (don't forget grep, awk, ack, etc)
01:24 diconzine oh
01:24 pyrimidine you should also learn some basic unix tools
01:24 diconzine i know them from shell script
01:24 diconzine perl use the same?
01:24 pyrimidine that's a start
01:24 diconzine :O
01:25 pyrimidine perl uses or emulates many unix commands, but it's better than that
01:25 diconzine i've been using unix for a few years, but only programming with C, Java and shell script
01:25 pyrimidine gotta go, dog needs to be walked (she's panicking)
01:26 diconzine never tried perl or pythin
01:26 diconzine :O
01:26 diconzine ok
01:26 diconzine thank u for explanations!
01:26 pyrimidine Java and C are great for some things as well
01:26 pyrimidine just not for text processing
01:26 pyrimidine afk & # walking dog
01:26 diconzine thats why i had to use shell script for some stuffs
01:26 diconzine rofl
01:26 diconzine cya
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03:21 CIA-94 biome: Chris Fields master * r3b82c87 / (5 files in 5 dirs): all locations working except one (and it isn't a legal one) - http://bit.ly/a8GcVK
03:29 CIA-94 biome: Chris Fields master * r9ee8602 / t/Segment/Simple.t : test updates that coincide with Segment changes - http://bit.ly/bSdCPI
03:29 CIA-94 biome: Chris Fields master * r43a60c3 / lib/Biome/Role/Segment.pm : get exceptions passing - http://bit.ly/aidO0R
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14:17 CIA-94 biome: Chris Fields master * rdf924bd / t/Factory/FTLocationFactory.t : bad test data; why was this even in bioperl???? - http://bit.ly/cPo6R5
14:17 CIA-94 biome: Chris Fields master * r08fde9c / (5 files in 5 dirs): all location tests passing - http://bit.ly/8Y4MTC
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16:11 deafferret .
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16:56 * deafferret chuckles   http://www.chipchick.com/wp-cont​ent/uploads/2009/04/sealand.jpg
17:05 pyrimidine my kind of place!
17:21 Jun Hi, pyrimidine. I havenot got your reply
17:22 Jun Do you have time next Monday or Tuesday?
17:25 Jun Anyway, I will wait for your reply. I am heading back home for the World Cup now. Have a nice weekend :D
17:26 pyrimidine Jun: Odd, I sent it off.  Monday is best.
17:26 pyrimidine Have fun watching the cup!
17:26 perl_splut ooh, next game is in 30 minutes
17:26 perl_splut I'm watching a rebroadcast of the concert from last night
17:28 Jun Weird, I have not got the email. Anyway, i will see u on Monday. Have fun too~ US is also in the World Cup tournament~
17:28 perl_splut first game is tomorow for them
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18:12 CIA-94 bioperl-live: Chris Fields master * r0fe10c5 / (6 files in 3 dirs): [bug 3099] initial msout Seq parser, courtesy Warren Kretzschmar - http://bit.ly/bLGi34
18:13 * perl_splut hides from the CIA *
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18:35 deafferret perl_splut: the Culinary Institute of America is harmless
18:36 perl_splut no it isn't
18:36 perl_splut it creates killers... why do you think they spend so much time practicing with knives...
18:36 perl_splut second game of WC is underway
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20:19 perl_splut 2 minutes left and still 0 - 0 Uru - Fra
20:21 deafferret isn't not scoring normal?
20:22 perl_splut and that is the game
20:22 deafferret 7 overtimes?
20:22 perl_splut ties are allowed
20:22 deafferret oh
20:22 perl_splut this isn't single elimination
20:23 perl_splut each team gets 3 matches the cumulative of their wins, ties and losses determines which 2 go to the next round from each group
20:24 perl_splut as for the lack of scoring. Yes that is normal.
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20:25 perl_splut but I prefer that to the idiocy of basketball where it seems to take no real effort to get the score up
20:29 CIA-94 biome: Chris Fields master * r80cb261 / t/Factory/FTLocationFactory.t : TODO now passes - http://bit.ly/9xo3Iz
20:29 CIA-94 biome: Chris Fields master * r591cc09 / lib/Biome/SimpleTypes.pm : add a SimpleTypes (non-MooseX::Type) class - http://bit.ly/asKmDu
20:29 CIA-94 biome: Chris Fields master * r0715b30 / (2 files in 2 dirs): shart/end_pos_type for SegmentContainer - http://bit.ly/cA1WEC
20:32 perl_splut sorry, anyways. back to bioperl stuff :)
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