Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-31

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All times shown according to UTC.

Time Nick Message
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08:43 daveb_ newbie's question:
08:43 daveb_ I have a GFF3 file where the last column sometime contains Note=...;locus_tag=...;... I would like to load this GFF3 file, pull out all the features of a certain type (i.e. CDS) that also have locus_tag=X, and get for each one it's starting position and length.
08:46 kblin haven't used the GFF format myself, but it sounds like it'd contain a sequence, right?
08:46 daveb_ It can, but mine is not. It only contain features. Similiar to gebank feature table.
08:51 kblin yeah, but I don't think that matters
08:52 daveb_ I don't even know how to load a local file (all I can find in the tutorial is using databases)
08:52 kblin ah
08:52 kblin look at Bio::SeqIO
08:54 kblin http://pastey.net/139118 loads an embl file
08:55 kblin you'll have to change the format used to whatever you need
08:57 kblin you can then iterate over the input "sequences" using while (my $seq = $in_seq->next_seq) {
08:57 kblin do stuff
08:57 kblin }
08:57 kblin if you only have one sequence in your file, that's only going to run once, obviously
08:58 kblin $seq has a list of SeqFeature objects
08:58 kblin you'd have to look at the api docs how to get at those
09:01 daveb_ After a little reading, I think I might need to use Bio::Tools::GFF, not Bio::SeqIO
09:04 kblin right
09:04 kblin gff seems special
09:04 kblin as I said, never used that
09:04 kblin Bio::Tools::GFF looks right for what you need
09:07 daveb_ now I have loaded the file, and I can iterate the features using my $feature = $parser->next_feature()
09:09 daveb_ This is supposed to return a Bio::SeqFeatureI implementing object. I tried print Dumper the features, just to get an idea how those 'Bio::SeqFeatureI implementing objects" look like, but all I get is something like: $VAR1 = 'Bio::SeqFeature::Generic=HASH(0xa111ed8)
09:14 kblin look at http://doc.bioperl.org/releases/biop​erl-1.4/Bio/SeqFeature/Generic.html
09:20 daveb_ ok, thanks. I'll take it from here. Cheers!
09:21 kblin np
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