Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-02-20

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All times shown according to UTC.

Time Nick Message
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01:49 driveby_bot /home/svn-repositories/bioperl: r16867 (cjfields) : Add id_mapper to SwissProt, and tests
01:49 driveby_bot Diff: http://tinyurl.com/yahlfsp
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01:51 driveby_bot /home/svn-repositories/bioperl: r16868 (cjfields) : add link for database
01:51 driveby_bot Diff: http://tinyurl.com/yzzz2k8
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02:37 deafferret ah, much better   http://clab.ist.unomaha.edu/svn_co​/CLAB/RT922/graphviz/overview.png
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06:47 kutie i have a question about perl
06:56 rbuels kutie: what can we do for you
06:56 kutie i want to read a fasta file
06:57 kutie but it wont ignore the >
06:57 kutie how do i write a script that will ignore the > for each sequence
06:57 rbuels kutie: have you installed bioperl?
06:57 kutie no i have installed the normal perl
06:58 rbuels kutie: well, you can use bioperl to do that, which is a set of perl libraries for doing this sort of thing (and lots of other stuff besides)
06:59 rbuels or if this is the only time you will need to do this, you can use regular perl too
06:59 kutie its the only time i will need to do this
06:59 kutie its for an assignment
06:59 rbuels haha, you should not have told me that, now i'm going to not give you the answer directly.   ;-)
07:00 rbuels because you have to *learn*
07:00 rbuels kutie: do you know perl regular expressions?
07:00 kutie some what
07:01 kutie i used this code but dont kno if it will work
07:01 kutie next if ($line =~ /^>/){;
07:01 rbuels that is malformed.
07:02 kutie really?? now im stuck
07:02 kutie :(
07:03 rbuels it's a straightforward syntax thing.
07:03 rbuels you are using the if statement in its postfix form. ...
07:03 rbuels so you don't need a {
07:03 kutie oh okay so if i just put next if ($line =~ /^>/); it will work
07:03 rbuels (and you don't need the parentheses either, but they will not cause an error)
07:04 rbuels well, it will ignore all lines that begin with >
07:04 kutie i also dont need to use the if statment in a loop or do i
07:04 rbuels well, you have to decide in some way whether to skip the line
07:04 rbuels there are other ways to express it ...
07:05 kutie like??
07:05 rbuels $line =~ /^>/ and next;
07:05 rbuels but the 'if' is clearer.
07:06 kutie i'm going to try it with out the if and see if it works
07:07 kutie programing is hard :(
07:08 rbuels lol.  it's easy once you get your brain to think in that way.
07:08 rbuels you could say that writing an english sentence is hard as well.
07:08 rbuels same thing, just a different language.
07:11 kutie it worked. thanks for the help
07:11 rbuels no problem.
07:12 kutie where can i download bioperl if i do want it for hte future
07:15 rbuels kutie: bioperl.org
07:16 kutie thanks
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