Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-06-14

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Time Nick Message
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07:39 Lynx_ pyrimidine: thanks, i'll look into it!
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10:09 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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11:35 Topic for #bioperl is now Be patient!  Sometimes it takes a few minutes for people to notice your question! | http://bioperl.org/wiki/IRC#Getting_help | http://www.bioperl.org/wiki/Using_Git | nopaste to gist.github.com
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14:22 T_antigen yay freenode is back
14:22 T_antigen gotta a tough one for you
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14:24 T_antigen So I am using the Bio::SearchIO::Writer::TextResultWriter; and trying to get the top-k hits from one blast report into another how would you do that?
14:25 T_antigen specifically what sub routine would you write to pass to Bio::SearchIO::Writer::TextResultWriter; under the key 'HIT'
14:26 dbolser why not write out an intermediate blast format file that just has the top k hits, then pass that to TextResultWriter ?
14:27 T_antigen whaaaa?
14:28 dbolser isn't blast in blast out quite easy?
14:28 T_antigen not sure what you mean by that
14:28 T_antigen yeah
14:28 dbolser http://www.bioperl.org/wiki/HOWTO:SearchIO
14:28 T_antigen but I need to filter out the top-k hits from one
14:28 T_antigen to create a new one with less hits
14:28 dbolser so ... create two search IO's one a reader and one a writer, then process the hits of one and write the filtered results to the other
14:29 dbolser http://www.bioperl.org/wiki/H​OWTO:SearchIO#Using_SearchIO # Golden
14:29 dbolser I don't think pages of a wiki should have a named author
14:29 T_antigen why not?
14:29 dbolser the wiki handles that meta data </aside>
14:30 dbolser perhaps acknowl. would be better </really this time>
14:36 T_antigen so I'm looking at ther esult object and it doesn't seem like I could just create one with my own hit list
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14:40 T_antigen I can't just pass part of a result object to the searchIO writer I have to give the writer the filter sub routine which takes the hit as an argument and returns a boolean wether to add it or not but theres no hit index so I can't get the top-k
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15:43 dbolser T_antigen: tricky
15:47 T_antigen yeah i thought so
15:47 T_antigen its okay tho
15:47 T_antigen boss says its unecessary now
15:48 T_antigen thought our 63 gig blast file says otherwise
15:48 T_antigen *though
15:49 dbolser T_antigen: can't you pass the writer one hit at a time?
15:51 T_antigen searchio only has write_result function'
16:23 dbolser hmmm
16:23 dbolser can you 'destroy' the hits you don't want in a loop?
16:40 perl_splut you can build up a new result object with just the hits you need
16:40 perl_splut http://doc.bioperl.org/bioperl-live​/Bio/Search/Result/BlastResult.html
16:40 perl_splut create a new object and add to it only the hits you want
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