Camelia, the Perl 6 bug

IRC log for #bioperl, 2013-06-11

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All times shown according to UTC.

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19:22 mj5q hello, quick question. Has anyone seen scripts for counting out x number of bp/aa from a position?
19:28 jhannah mj5q: sure. do you have a Seq object already?
19:30 mj5q hi, I'm a newbie. I have both the aa position and the associated FASTA file with the variant inserted - from ANNOVAR program if you are familiar with it. So I do not know if any of that qualifies as a Seq object
19:39 jhannah mj5q: well, so first you'll want to create a Seq object from the FASTA file http://www.bioperl.org/wiki/HOWTO:SeqIO
19:40 jhannah then you'd call $seq->subseq() to get whatever position you cared about  https://metacpan.org/module/CJFIELD​S/BioPerl-1.6.901/Bio/Seq.pm#subseq
19:48 mj5q thank you. Would the subseq(10,40) include all positions between 10 and 40?
19:49 jhannah mj5q: yessir
19:49 jhannah or madame
19:49 jhannah :)
19:49 jhannah madam?
19:49 jhannah I don't know how to spell 'madam'... :)
19:55 mj5q haha thanks for your help, I'll be back tomorrow
19:55 jhannah mj5q: k :)
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