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

[Martin Morgan]

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

> 
> 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