Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-01-10

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All times shown according to UTC.

Time Nick Message
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17:19 jessicajames Is there anyway I can download a bunch of PDB files from proteins that are known to be stable? I wrote this algorithm that tests stability of proteins and want to test it on stable and unstable proteins to see if to see if it works!
17:34 rbuels jessicajames: i would start by investigating what web service APIs the PDB makes available
17:35 rbuels jessicajames: there might be some wrappers for them in bioperl, maybe ...
17:35 * rbuels looks
17:35 jessicajames thanks for checking rbuels - I'm just having a hard time finding what I need
17:37 rbuels jessicajames: i assume you have googled for things like 'bioperl PDB' and 'bioperl protein data bank'
17:38 rbuels jessicajames: having googled for that, i find that somebody has written some CPAN modules called WWW::PDB
17:38 rbuels which may or may not be helpful and/or up to date
17:38 jessicajames okay
17:38 jessicajames I'll look into it
17:38 jessicajames I guess my question was more #bioinformatics related
17:39 jessicajames but I appreciate your help and time :)
17:39 rbuels jessicajames: you mean my googling something for you and telling you what was on the google page?  lol
17:39 rbuels jessicajames: you're welcome.  ;-)
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17:40 jessicajames lol
17:40 jessicajames well
17:40 jessicajames there's only 20 people in this channel
17:40 jessicajames so I thank you for acknowledging my existence
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18:07 dnewkirk Are you asking about APIs? Or how to find those that are stable specifically?
18:13 jessicajames Well basically I just wanted a list of thermostable proteins and their corresponding less-stalbe mutants
18:13 jessicajames something like that
18:19 dnewkirk Checking with some others in our group to see what I can find.
18:30 jessicajames dnewkirk, thank you
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19:08 leont That 'installing BioPerl into a personal module area' section should probably be rewritten to modern standards
19:08 leont Quite frankly, there's no reason not to use local::lib, but there are lots of reasons for not using PREFIX.
19:09 Jaquin joined #bioperl
19:10 Jaquin HI everyone
19:10 jessicajames herro Jaquin
19:10 Jaquin does anyone here can help me write a bioperl program which search for words from specified file
19:11 jessicajames what do you mean?
19:11 jessicajames what OS are you on?
19:11 Jaquin linux
19:11 jessicajames why not just use grep?
19:12 leont Or ack
19:12 Jaquin sorry im complete rookie at this :) idk whats grep or ack :D
19:12 jessicajames go into the terminal and type 'man grep'
19:12 Jaquin besides its a kind of a homework :)
19:12 Jaquin and i need to create my own simple prohram
19:12 Jaquin *program
19:13 Jaquin i use those commands
19:13 jessicajames Basically, grep usage is: "grep <text you're searching for> <filename>"
19:13 Jaquin open (DANE3,"< /home/biol19/tekst.txt")  or die "Nie znaleziono pliku\n" ; print "======================================\n" ; while (<DANE3>) { $tekst="$_" ; print "$tekst" ; # substitution if ($tekst =~ /Anna/) { print "$tekst" ; $tekst =~ s/Anna/Joanna/ ; print "$tekst" ;} }
19:13 Jaquin it bassicly should open file tekst.txt
19:14 Jaquin and it do this
19:14 jessicajames you should pastebin that or something
19:14 dnewkirk can you post the code to pastbin please?
19:14 jessicajames idk about others, but i'm not going to try to read that
19:14 Jaquin then it should change every word from file "Anna" to "Joanna
19:14 Jaquin but it doesnt do anything like that
19:14 dnewkirk We need the code in a readible format to help.
19:14 Jaquin ok how do i paste it here :)
19:15 Jaquin pastbin? whats that?
19:15 leont Jaquin: that is the old form of open, I think you may want to use the new form, to avoid certain kinds of magic and scoping issues
19:15 jessicajames Jaquin, look at lexical file handles
19:16 dnewkirk paste the code into pastebin (http://pastebin.com/) and then post the link here
19:16 leont «open me $dane3,'<', '/home/biol19/tekst.txt' or die …»
19:16 leont oops, me should be my
19:16 Jaquin http://pastebin.com/1idxRMFy
19:18 dnewkirk Are there more than one instance of Anna per line?
19:18 Jaquin Nope "Anna" is just once in second line
19:28 Jaquin Ok let me start from the begining, Ill try to explain what I need
19:29 dnewkirk no need, I know what you want I think
19:29 Jaquin i need to write a program which counts the number of specified words in file
19:30 Jaquin the thing i showed you was something else i tried instead but i thing that counting words will be easier to do
19:30 Jaquin *think
19:31 Jaquin it has to count specified words and at the end show the number of how many those words are there :)
19:32 dnewkirk http://pastebin.com/Wi3hKV8j
19:34 Jaquin wow thanks
19:34 Jaquin ill try it out
19:36 dnewkirk You should be able to modify your code to do the word counts pretty easily.
19:37 Jaquin to be honest i never seen those commands you wrote me, i used the one I showed you
19:37 dnewkirk Sorry, I should have commented the lines better.
19:39 Jaquin no need i can search those commands you helped mi a lot
19:39 Jaquin thank you very much
19:40 Jaquin ill have to look for those counting commands too
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