On Wed, May 12, 2010 at 10:22 PM, Fahim Md <fahim.md@gmail.com> wrote:

> Does anyone know how to read a .psl file( .psl is an blat output file) in
> R???
> The .psl format is as follows(enclosed by #-line):
> ########
> psLayout version 3
>
> match    mis-     rep.     N's    Q gap    Q gap    T gap    T gap
> strand    Q            Q       Q        Q      T            T       T
> T      block    blockSizes     qStarts     tStarts
>         match    match           count    bases    count    bases
>    name         size    start    end    name         size    start
> end    count
>
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> 25    0    0    0    0    0    0    0    +    1367452_atAAAAAABBBBBBBBB
> 25    0    25    chr11    87759784    81380087    81380112    1    25,
> 0,    81380087,
> ----
> ----
> ---
> #######
>
>
> I dont want to use file() followed by incremental readLines() function.
> Does anyone know of any package dealing with it or any alternative?
>

See read.table() and the skip argument.

Sean

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