[BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?

[Steve Lianoglou]

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.

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
>



-- 
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