Bioperl Graphics question

wackattack has asked for the wisdom of the Perl Monks concerning the following question:

Replies are listed 'Best First'.
Re: Bioperl Graphics question by jbrugger (Parson) on Jul 06, 2005 at 05:05 UTC
Have you installed all needed modules? i just installed bioperl ( apt-get install bioperl ), copied exactly your code, created the 'data1.txt' file exactly as given in the tutorial (copy paste), ran `perl test.pl data1.txt > test.png`, and got the proper output, like the example png, including the text. There seems nothing wrong with your script, it has to be the installation. ps. i commented out the 'use lib' line. "We all agree on the necessity of compromise. We just can't agree on when it's necessary to compromise." - Larry Wall.	[reply] [d/l]
Re: Bioperl Graphics question by chromatic (Archbishop) on Jul 06, 2005 at 05:10 UTC
Assuming you have the modules installed correctly so that `perldoc` can find them, use `perldoc -l` to show the installed location and `perldoc -m` to view the module's code in your pager program.	[reply] [d/l] [select]
Re: Bioperl Graphics question by monarch (Priest) on Jul 06, 2005 at 04:28 UTC
It would appear, for whatever reason, the `-label` argument isn't being interpreted as being true. Yet you seem to set it just as the tutorial example showed. I could not find the `Bio::Graphics` module in CPAN, so I couldn't look up the documentation (occasionally tutorial code examples are wrong and it helps to track down the documentation directly). You may be able to find the module in something like: `/usr/lib/perl5/site_perl` [download] and running `find . \|grep Bio \|grep Graphics` [download] Alternatively if you're on windows, open explorer, go to your Perl installation directory (`C:\Perl\`?) and then from the explorer window right-click on the directory name, select search, and type in `Graphics.pm`.	[reply] [d/l] [select]
Re^2: Bioperl Graphics question by biosysadmin (Deacon) on Jul 06, 2005 at 13:21 UTC
Bio:::Graphics is a namespace for a set of modules used for drawing images common to Bioinformatics. On my machine it's located in the directory `/usr/local/lib/perl5/site_perl/5.8.6/Bio/Graphics`. You could poke around there (or somewhere similar) if you'd like a peek at the source code. Probably the most reasonable thing to do would be to e-mail the Bioperl mailing list (there's a link off the website) and tell them your problem. Also, you might try some of the later examples in the tutorial and see if those work for you. I ran the example using both sets of code and got the image with labels on it, so I don't know what the problem would be. What OS and Bioperl version are you using? Bioperl makes heavy use of the GD Perl package, what version of GD are you using?	[reply] [d/l]
Re: Bioperl Graphics question by virtualsue (Vicar) on Jul 06, 2005 at 05:02 UTC
2nd question: Any clue as to how I can find the package where this is installed to look at it's source code? You have a "use lib" directive in your code. Perhaps the Bio modules are somewhere under /home/lstein/projects/bioperl-live .	[reply]
Re^2: Bioperl Graphics question by biosysadmin (Deacon) on Jul 06, 2005 at 13:13 UTC
That's actually from Lincoln Stein's code, he's the author of the tutorial and also the author of the CGI.pm module.	[reply]
Re^3: Bioperl Graphics question by virtualsue (Vicar) on Jul 06, 2005 at 18:32 UTC
No doubt, it's just that the line appeared in wackattack's code, not the code he said he used as a reference for using the Bio modules. I do know who Lincoln Stein is, but I wondered if in following some other example a little too closely, the Bio modules had been installed in an unconventional place on wackattack's system. That sort of thing occasionally happens. For the original poster, the special global array @INC contains the paths which perl uses to find scripts and libraries for "do filename;", use and require commands. This is just general information, and isn't nearly as useful as perldoc -l (per chromatic). :) `perl -e 'print "$_\n" for @INC'`	[reply] [d/l]