Hi Steve, On 08/27/2010 09:16 PM, Steve Lianoglou wrote: > Hi Herve, thanks! > > Honestly, I feel like there is only so much you can do, with respect > to a "perfect heuristic". > > As long as there is *some* overlap between the seqnames from the query > and subject sequences, there's got to be *some* consistency, right? > > A warning seems more than appropriate, and I guess I'd expect an error > only when there is *no* overlap between subject and query seqnames ... Yes I was thinking of something along those lines too. I just went for the quickest fix for now. I'll try to improve this when I'm back from vacations (after Labor Day). Thanks for the feedback! Cheers, H. > > Anyway, thanks again folks! > > -steve > > 2010/8/27 Hervé Pagès<hpages at="" fhcrc.org="">: >> Hi Steve, >> >> Until we come up with the perfect heuristic for this, I've modified >> findOverlaps() and its related methods so that they issue a warning >> instead of an error when 'query' and 'subject' don't appear to use >> a similar seqname convention. >> >> This is in GenomicRanges version 1.0.9 (release) and 1.1.23 (devel). >> >> Cheers, >> H. >> >> >> On 08/24/2010 09:35 AM, Steve Lianoglou wrote: >>> >>> Hi Martin, >>> >>> On Tue, Aug 24, 2010 at 12:14 PM, Martin Morgan<mtmorgan at="" fhcrc.org=""> >>> wrote: >>>> >>>> On 08/24/2010 08:16 AM, Steve Lianoglou wrote: >>>>> >>>>> Hi, >>>>> >>>>> Sorry to be a pest about this, but could we get some traction on this? >>>>> >>>>> I've temporarily commented out the isArabic regex test to get around >>>>> this issue as a work around, but want to keep my own/analysis code in >>>>> line w/ the real GenomicRanges package. >>>> >>>> We've discussed this locally and will make changes this week. Martin >>> >>> Sweet. >>> >>> Thanks Martin (+ co), >>> >>> -steve >>> >>>> >>>>> >>>>> Thanks, >>>>> -steve >>>>> >>>>> >>>>> On Fri, Aug 20, 2010 at 12:53 PM, Steve Lianoglou >>>>> <mailinglist.honeypot at="" gmail.com=""> wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> The GenomicRanges:::.similarSeqnameConvention function is returning >>>>>> FALSE where, IMHO, it shouldn't be. >>>>>> >>>>>> I've landed in a situation where this function is called with the >>>>>> following values for seqs1/2: >>>>>> >>>>>> seqs1: >>>>>> [1] "chr1" "chr1_random" "chr10" "chr10_random" >>>>>> "chr11" "chr11_random" >>>>>> [7] "chr12" "chr13" "chr13_random" "chr14" >>>>>> "chr15" "chr15_random" >>>>>> [13] "chr16" "chr16_random" "chr17" "chr17_random" >>>>>> "chr18" "chr18_random" >>>>>> [19] "chr19" "chr19_random" "chr2" "chr2_random" >>>>>> "chr20" "chr21" >>>>>> [25] "chr21_random" "chr22" "chr22_random" "chr22_h2_hap1" >>>>>> "chr3" "chr3_random" >>>>>> [31] "chr4" "chr4_random" "chr5" "chr5_random" >>>>>> "chr5_h2_hap1" "chr6" >>>>>> [37] "chr6_random" "chr6_cox_hap1" "chr6_qbl_hap2" "chr7" >>>>>> "chr7_random" "chr8" >>>>>> [43] "chr8_random" "chr9" "chr9_random" "chrM" >>>>>> "chrX" "chrX_random" >>>>>> [49] "chrY" >>>>>> >>>>>> seqs2: >>>>>> [1] "chrY" >>>>>> >>>>>> and it looks like the "isArabic" function in funList is the culprit >>>>>> here. Perhaps this regex test is so necessary, given all the other >>>>>> tests that are being run?. >>>>>> >>>>>> I guess it's not so easy to come up w/ a perfect heuristic for this >>>>>> function to check "comparable seqnames", but IMHO, it seems as if my >>>>>> scenario should pass as a "good" (ie. the conventions are similar). >>>>>> >>>>>> Another scenario would be to just have this function return TRUE when >>>>>> the intersection between seqs1 and seqs2 is length 0. I guess that >>>>>> must be too simple though ... >>>>>> >>>>>> -- >>>>>> Steve Lianoglou >>>>>> Graduate Student: Computational Systems Biology >>>>>> | Memorial Sloan-Kettering Cancer Center >>>>>> | Weill Medical College of Cornell University >>>>>> Contact Info: http://cbio.mskcc.org/~lianos/contact >>>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Martin Morgan >>>> Computational Biology / Fred Hutchinson Cancer Research Center >>>> 1100 Fairview Ave. N. >>>> PO Box 19024 Seattle, WA 98109 >>>> >>>> Location: Arnold Building M1 B861 >>>> Phone: (206) 667-2793 >>>> >>> >>> >>> >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319