Perl 6 - the future is here, just unevenly distributed

IRC log for #bioperl, 2016-06-10

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Time Nick Message
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14:31 Guest104 hello, I have a problem, I use Index::GenBank, but the indexed sequence has length of 0. see the code http://pastie.org/private/pjfbuiouotga4sfhyfpew
14:31 Guest104 Any ideas?
14:31 Guest104 lines 28, 29
14:35 Guest104 anyone?
15:52 trs Guest104: is there actually a sequence in the index called "CP002684"?
15:58 Guest104 trs, I found that SeqIO does not read my file correctly
15:58 Guest104 minimal source : http://pastie.org/private/x7c4nuf7nzozkzmpruibw
16:02 trs Nopaste the contents of sequence2.gb?
16:06 Guest104 http://www.ncbi.nlm.nih.gov/nuccore/CP0​02684.1?report=genbank&log$=seqview
16:06 Guest104 downloaded from here
16:06 Guest104 genbank full
16:10 trs That file doesn't actually contain any nucleotide or amino acid data.
16:12 Guest104 are you sure?
16:12 trs It looks like it's an annotation-only record that pulls in other GenBank records.
16:12 trs Take a look at it yourself.
16:12 trs There's only references to other GenBank records, no sequence data in the file I got.
16:14 trs If you download as a fasta, GenBank pieces together the bits.
16:15 trs At least that what seems to be happening for me, and it's consistent with my understanding of GenBank.
16:15 Guest104 I am sorry, I am new to bioinformatics :( so is there a way to get a sequence
16:15 trs Download as a "FASTA" rather than "GenBank (full)".
16:15 Guest104 One more question
16:16 Guest104 If I need to get gene locations FASTA wont work, right
16:16 Guest104 ?
16:17 Guest104 As I cant see any gene annotations in fasta file
16:18 trs Correct.  But you can use the fasta sequence to back the annotations from genbank.
16:19 trs (In theory.  I'm not sure off the top of my head how you'd do that in BioPerl.)
16:19 trs (I don't really use BioPerl... but I do use Perl for biology a lot. :-)
16:20 Guest104 So you are saying, that I need to download fasta and genbank file. |GenBank file will provide the gene positions, and fasta the sequences?
16:20 trs That would be one way I might tackle the problem, yes.
16:21 trs Of course, I'm not sure what the end goal is, so maybe there's a better way than what I've suggested off the cuff.
16:22 Guest104 The idea is to check if some sequence genes exist in other nuc. sequence
16:22 Guest104 ..sequence of genes..
16:23 Guest104 so I need to get gene sequences
16:25 Guest104 by the way, where do you use BioPerl in biology?
16:26 trs I don't really use BioPerl.  But I do use Perl for biology.
16:26 trs at the University of Washington.
16:27 trs which is in Seattle, Washington in the USA.
16:27 Guest104 I am sorry, I did mean just Perl :)
16:30 Guest104 I know where Washington is :)
16:34 trs I try not to assume too much. :-)
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