Camelia, the Perl 6 bug

IRC log for #bioruby, 2012-10-20

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All times shown according to UTC.

Time Nick Message
08:18 lintsu shevy: yeah :)
08:19 lintsu shevy: can you help me with this error http://i.imgur.com/j65ma.png
08:20 lintsu shevy: ff = Bio::FlatFile.new(Bio::FastaFormat, ARGF) <- I don't know what I should give to ARGF
09:58 shevy hmm
09:58 shevy ARGF is a constant
09:58 shevy lintsu, have a look at this documentation briefly please: http://www.ruby-doc.org/core-1.9.3/ARGF.html
09:59 shevy In short, "ARGF is designed for use in scripts that process files given as command-line arguments or passed in via STDIN."
10:00 shevy lintsu usually I think this requires a commandline argument
10:00 shevy let's say your file is called foobar.rb ok?
10:00 shevy ruby foobar.rb this_file.txt
10:00 shevy and then I assume that Bio::FlatFile.new() will read in that file
10:00 shevy let me check on the API of this class
10:01 lintsu shevy: yeah I have looked that. but I'm new to coding as well so not all is clear to me
10:01 shevy Here documentation: http://bioruby.org/rdoc/Bio/FlatFile.html
10:01 lintsu shevy: and I use Shoes to run my code and not commandline. I think that makes some hussle as well
10:01 shevy .new accepts two arguments:
10:01 shevy new(dbclass, stream)
10:01 shevy The argument stream has this: "Same as ::open, except that ?stream? should be a opened stream object (IO, File, ?, who have the ?gets? method)."
10:02 shevy lintsu, hmm
10:02 shevy yeah the error looks a bit odd
10:02 shevy but at least ruby works on your system, so that is a plus :)
10:02 shevy I think the error means that you pass in a string, and String has no .getc method
10:03 lintsu ah yeah that is true
10:03 lintsu that I'm trying to pass string
10:03 shevy did you try to use it differently?
10:03 lintsu my code now looks like http://pastebin.com/RwkDAZYt
10:03 shevy hmm you can simplify this code a bit
10:03 shevy @sequenceCount = @sequenceCount + 1
10:03 shevy is the same as:
10:04 shevy @sequenceCount += 1
10:04 shevy combinedText = combinedText + File.read(file)
10:04 shevy can become:
10:04 shevy combinedText << File.read(file)
10:04 shevy lintsu, can you use irb?
10:04 shevy or pry?
10:04 lintsu yeah
10:05 shevy hmm may be easier to test ff = Bio::FlatFile.new() in irb first
10:05 shevy btw I just tried it in irb
10:05 shevy this works fine:
10:05 shevy Bio::FlatFile.new Bio::FastaFormat, 'peoples_age.yml'
10:10 lintsu hmm what the h.. I can't cd the dir I have my sequences
10:13 lintsu plah ruby isn't working.
10:51 lintsu ah, now it is working agay. yay for backups
11:05 shevy hehe
11:05 shevy how can you not cd to the dir :)
11:06 shevy backups are really a must
11:06 shevy I once accidentally removed / hahaha
11:06 shevy but it was because of a TAB press, and readline completing it to " /"
11:06 lintsu there is space in folder name, but i haven't have that difficult before
11:06 lintsu hah :D
11:06 shevy since that day I (a) always keep backups (b) am careful when I press TAB key
11:06 shevy was in 2003, has not happened again :)
11:07 lintsu i removed /usr/bin/ruby because Internet said to remove it :D
11:07 shevy yeah lintsu ' ' in folder names can be annoying
11:07 shevy waaaah?
11:07 shevy hahaha
11:07 shevy you kill the binary and then ruby does not work anymore haha :D
11:07 lintsu yeah..
11:07 shevy do you use ruby 1.9.x version? or still 1.8.x branch
11:07 shevy I am still usually using 1.8.x :\
11:08 shevy Encoding annoys me, I do not use UTF-8
11:08 lintsu i tried to unistall ruby and so on... but because that comes with operating system it wasn't good
11:08 lintsu 1.9.3
11:09 shevy aha
11:14 lintsu /usr/local/rvm/gems/ruby-1.9.3-p194/gems/bi​o-1.4.3/lib/bio/io/flatfile/buffer.rb:34:in `path': No such file or directory - sequence/13B9SAB004_G2.txt (Errno::ENOENT) from /usr/local/rvm/gems/ruby-1.9.3-p194/gems/bi​o-1.4.3/lib/bio/io/flatfile/buffer.rb:34:in `for_io' from /usr/local/rvm/gems/ruby-1.9.3-p194/gems​/bio-1.4.3/lib/bio/io/flatfile.rb:230:in `initialize' from miip.rb:3:in `new'
11:14 lintsu fro miip.rb:.3:in `<main>'
11:16 lintsu this is like trying to walk in dark
13:39 shevy hmm
13:39 shevy you really use strange combinations man
13:39 shevy rvm ... shoes ...
13:39 shevy :)
13:39 shevy I use ruby straight compiled from the source
13:40 shevy I think the error says that buffer.rb expected a file
13:40 shevy "sequence/13B9SAB004_G2.txt"
13:40 shevy but it could not find it
13:40 shevy I dont know what this file is
13:40 shevy you could try to locate it 13B9SAB004_G2.txt
13:40 shevy Errno::ENOENT means that it does not exist (at that position)
13:40 shevy all errors in ruby are bundled into the Errno module constant
13:41 shevy for instance, if you lack permissions to access a file, the error Errno::EACCES will be raised
13:41 shevy lintsu, don't worry, in some days you'll be able to read those error messages easily :)
13:42 lintsu shoes is easy way to do gui apps
13:43 shevy hehe I found it hard! :)
13:44 shevy but if it works for you that is good
13:44 shevy (I ran into some problems back then with it)
13:44 lintsu yay now I managed to give that file to it :D
13:45 lintsu /Users/linnea/projects/Shoes/Sequence cleaner/sequences/13B9SAB004_G2.txt:1: syntax error, unexpected '>'
13:45 lintsu shouldn't fasta file start with >?
13:45 shevy yeah
13:46 shevy but it may be that this is interpreted as ruby code
13:46 shevy and ruby expects a > to be used in a comparison
13:46 shevy if 5 > 4
13:46 shevy puts 'yes 5 is larger than 4'
13:46 lintsu yeah
13:46 lintsu but this is just the expample code I took from tutorial :P
13:46 shevy do you have a link to it?
13:46 shevy so I can verify
13:47 lintsu http://thebird.nl/bioruby/Tutorial.rd.html
13:47 shevy or tell me where or which ... ah ok
13:47 lintsu after "For example, in turn, reading FASTA format files:"
13:47 shevy ok
13:47 shevy let me remember where I keep my own fasta files ... hehehe
13:49 shevy ok found one .ffn file
13:49 shevy interesting
13:49 shevy that example does not work for me
13:50 shevy NoMethodError: private method `getc' called for "NC_005213.ffn":String
13:50 shevy very strange
13:50 shevy here is github bioruby btw https://github.com/bioruby/bioruby
13:50 shevy I will file an issue
13:56 lintsu :)
13:56 lintsu do you know any programmes that use bioruby?
13:59 shevy lintsu hmm there is pjotr
13:59 shevy see http://www.biogems.info/
13:59 shevy the more people use it, the better it will become
13:59 shevy you can look for "Pjotr Prins" there
14:00 shevy I myself wrote mostly standalone little things
14:00 shevy nothing really that useful :\
14:00 shevy I wanna do virtual cells one day
14:05 lintsu i'm trying to replace excel macros for our lab
14:06 lintsu shevy: what timezone you live in? you seem to be awake 24 h a day :D
14:07 shevy lintsu today is saturday. I am in central europe
14:07 lintsu explains :)
14:07 lintsu i'm in finland
14:07 shevy suomi!!!
14:07 lintsu yeah :D
14:07 shevy do you know janne ahonen?
14:08 shevy we here believe that all fins are like him :D
14:08 lintsu yeah he is ski jumper?
14:08 shevy yeah hehe retired though :(
14:08 shevy all my old heroes retired :P
14:08 lintsu yeah
14:08 lintsu you are from switzerland? :D
14:09 shevy almost! austria
14:09 shevy swiss and people from bavaria (southern germany) are ok, the northern germans and austrians usually don't get along too well, it's the language that keeps us separate :P
14:10 lintsu heh yeah
14:10 lintsu it's almoust same with us and swedens and russians
14:10 shevy hahaha :D
14:10 shevy well I understand russians, but swedes?
14:11 lintsu finland was part of them while back :P
14:11 shevy I think most fins I knew were from Helsinki, one guy though went to some other place... I think to a university, studied physics ... not sure where
14:11 shevy I only remember he had to wait like 30 minutes for a night bus in order to reach home again
14:11 lintsu i live in turku
14:11 shevy turkey!
14:11 shevy hehe
14:11 lintsu hmmm.. maybe he went to espoo, it's next to helsinki :P
14:11 shevy never heard that... but that's a funny name
14:11 lintsu :P
14:12 lintsu we were design capital of last year!
14:12 lintsu or culture..
14:12 lintsu hmm i think culture :D
14:12 shevy 'The Finnish name Turku originates from an Old East Slavic word, t?rg?, meaning "market place"'
14:12 shevy cool
14:12 lintsu oh I had forgoted that
14:13 shevy I always wanted to visit Helsinki
14:13 shevy but I am scared of bad weather and coldness :(
14:13 lintsu I don't think it's so cold to compared to austria :D
14:13 shevy we used to be in goteborg, in sweden, many years ago. there was constant fog and it was quite cold ... I could not see far ahead
14:13 shevy hehe
14:13 lintsu and if you come by summer.. less snow ;)
14:13 shevy well western austria can be very cold due to the mountains
14:13 shevy eastern austria is semi-ok
14:14 shevy remember, italy is not that far away! (northern italy... trieste, used to belong to austria once hehe)
14:14 lintsu hehe yeah
14:14 shevy ok summer then
14:14 lintsu i prefer south italy :)
14:14 lintsu but it's really hot there
14:14 shevy hehe
14:15 shevy yeah
14:15 shevy I think northern italy... east or west is perfect
14:15 shevy not too hot, great food, even lakes or the ocean
14:15 shevy like near the Dolomite mountain area... southwest of it near the mediterranean sea
14:15 shevy btw!
14:15 shevy some folks here are from Italy
14:16 shevy like gianlucadv
14:16 shevy or Helios... he is from milano I think
14:16 lintsu ah ok :)
14:16 shevy seems most other italian bioruby users are from milano as well
14:16 lintsu good to see that some italian are good with computers :D
14:17 lintsu i have only seen those "ciao a tutti" people
14:17 lintsu okay few nice people too
14:17 shevy hehe there are quite a few of them actually
14:17 shevy but often they speak only italian
14:17 lintsu (i'm half italian so I think I have right to say those things :D)
14:17 shevy yeah, they come to #ruby say ciao... then ask in italian whether anyone speaks italian... then they quit
14:17 shevy cool
14:18 shevy italian food <--- rocks
14:18 shevy how is food in suomi? :)
14:19 lintsu good I think :D
14:53 lintsu nom nom we are gonna make waffles with my friend tonight.. but they aren't finnish food I think :D
15:21 shevy hehehe
15:21 shevy well
15:21 shevy I like special food from different countries
15:22 shevy in korea, they have a hot pot with rice and vegetables and such
15:22 shevy the cool thing is, the rice gets harder on the surface of the pot, and tastes differently :)
15:22 shevy that is one way of doing it http://cdn.biggestmenu.com/00​/00/42/b43ad69ae709b2c3_m.jpg
15:23 shevy does not look like much, but that pot is really super hot, and the food on the contact with the surface tastes differently
15:36 lintsu traditional finnish wood is strange :D
15:36 lintsu a lot grease and not much spices
15:57 shevy wait what
15:58 shevy you guys eat wood????
15:58 shevy wow :)
15:58 shevy I knew fins were tough, but THAT tough is a big surprise
16:02 lintsu :D
16:02 lintsu haha i mean food
16:03 lintsu oh it's look better than I though
16:03 lintsu http://en.wikipedia.org/wiki/Finnish_cuisine
16:12 shevy coool
16:12 shevy wonder if there are any finnish shops in austria haha :D
16:20 lintsu in german there is I think
16:20 lintsu you should try salmiakki
16:20 lintsu it so goood
16:20 lintsu http://www.salmiyuck.com/
17:58 shevy joined #bioruby
18:27 shevy lintsu, that can be eaten???
18:27 shevy salmiak ... that sounds like NH4CL ... Ammonium chloride
19:19 lintsu :D
19:19 lintsu yeah it is
19:20 lintsu its nomnom

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