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Re: bioperl newbie's question: simple GFF3 peocessing

by BioLion (Curate)
on Jul 31, 2010 at 09:23 UTC ( #852232=note: print w/replies, xml ) Need Help??


in reply to bioperl newbie's question: simple GFF3 peocessing

Hi daverave, you can do all you want and more using BioDB::GFF and the related Bio::DB::GFF::Feature. These will let you load a GFF file into a database (which can be in memory if you want) and extract features of whatever type you like and also sub-group them by attributes.

There is example code for doing much of this on their respective CPAN pages, so have a go, see how far you get and come back to us if you are still struggling - remember to include code/input/error messages/output that you write/use/get/want.

Good luck - hope this helps.

Just a something something...

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Re^2: bioperl newbie's question: simple GFF3 peocessing
by daverave (Scribe) on Jul 31, 2010 at 09:41 UTC
    Thank you very much BioLion.

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[Lady_Aleena]: And the env variable $HOME doesn't work either. !@#$
[shmem]: no, that's a shell feature. Use $ENV{HOME}
[marioroy]: my $ans = qx{ find \$HOME -name "*.pl" -exec ls -l {} \\; };
[marioroy]: must backslash $ inside qx
[Lady_Aleena]: I haven't written perl for a while, I've been trying to do things at the command line. I'm having to relearn a lot.
[marioroy]: LA can you post the qx find again
[Lady_Aleena]: Things I would have written a script for while I was on Windows, I can run simply on the command line.
[Lady_Aleena]: marioroy, my @music_times = qx(find ~/Music/Albums/ -type f -iname '*.mp3' -exec mp3info -p "%S\n" {} \;); #unfixed

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