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

[Steve Lianoglou]

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
>



-- 
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