[BioC] GenomicRanges:::.similarSeqnameConvention regular expressions needs some tweaking?
Steve Lianoglou
mailinglist.honeypot at gmail.com
Tue Aug 24 17:16:40 CEST 2010
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
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