Hi
Thanks for reply

RefSeqID               targetName    strand        blockSizes
queryStart             targetStart
XM_001065892.1    chr4                 +            127,986,
0,127,                  124513961,124514706,
XM_578205.2         chr2                  -             535,137,148,
   0,535,672,            155875533,155879894,155895543,
NM_012543.2         chr1                 +             506,411,212,494,
0,506,917,1129,    96173572,96174920,96176574,96177991,

Is each "block" for each RefSeqID treated individually, or do you want one
overlap to count for all of them?
*Ans: I am looking for the  latter option and want one overlap to count for
all of the blocks.  For example, If I am given the following  sequence with
its alignment
UnknownSeq           targetName    strand        blockSizes
                  queryStart                      targetStart
XM_ABCD                chr4                 +            100, 200, 500
          0,200, 1200                  124513961,124514706, 124515900

I am interested in finding which of the three RefSeqIDs above overlaps with
the given unknown sequence. The obvious answer  is the first refseqID
(XM_001065892.1).


Lastly -- how are these ranges defined?
Is the first row supposed to be turned into:
* The intervals on the target genome for each unknown sequence can be found
using blockSizes and targetStart. For me, the "queryStart" field  above is
redundant and wont be used. The first row may be
The intervals in the first row may be found using (targetStart + blockSizes
-1)
chr4 (124513961) -- (124513961 + 127 -1)
chr4 (124514706) -- (124514706 + 986 -1)

Thanks again
Fahim


On Tue, May 31, 2011 at 12:05 PM, Steve Lianoglou <
mailinglist.honeypot@gmail.com> wrote:

> Hi,
>
> On Tue, May 31, 2011 at 11:08 AM, Fahim Mohammad <fahim.md@gmail.com>
> wrote:
> > Hello
> > I have a file containing a list of aligned Refseq identifier in the
> > following format.  I want to convert this file into RangedData format in
> > such a way that  "findOverlaps" function be as efficient as possible. I
> know
> > how to do this when each of the identifiers has just a start and an end
> > coordinate. IRanges package is very efficient in finding the overlapping
> > intervals in such case. But when the structure is in the form of blobs
> (as
> > shown below in the last three fields), I am not sure how to convert this
> > structure into RangedData format and how to subsequently call the
> > "findOverlaps" function.
> >
> > RefSeqID               targetName    strand        blockSizes
> > queryStart             targetStart
> > XM_001065892.1    chr4                 +            127,986,
> > 0,127,                  124513961,124514706,
> > XM_578205.2         chr2                  -             535,137,148,
> >   0,535,672,            155875533,155879894,155895543,
> > NM_012543.2         chr1                 +             506,411,212,494,
> > 0,506,917,1129,    96173572,96174920,96176574,96177991,
>
> I guess the answer lies in how you want overlaps to be calculated.
>
> Is each "block" for each RefSeqID treated individually, or do you want
> one overlap to count for all of them?
>
> If the answer is the latter, you might consider putting the intervals
> into a GRangesList object, where each element in the list is a GRanges
> object that has all the ranges for the particular refseq id ... if you
> want them all individually, then you just have to parse it into a
> GRanges object.
>
> If you're asking *how* to parse the file, there are many ways. I'd
> maybe use a read.table to get this thing into its respective columns,
> then iterate over each row converting it into a GRanges object that
> has as many ranges as "blocks" -- look at ?strsplit if you don't know
> how to do that.
>
> Lastly -- how are these ranges defined?
> Is the first row supposed to be turned into:
>
> chr4 (124513961) -- (124513961 + 0 + 127)
> chr4 (124514706 + 127) -- (124514706 + 127 + 986)
>
> or?
>
> -steve
>
> --
> 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
>



-- 
Fahim Mohammad
Bioinforformatics Lab
University of Louisville
Louisville, KY, USA
Ph:  +1-502-409-1167

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