On Thu, May 13, 2010 at 12:31 PM, Fahim Md <fahim.md@gmail.com> wrote:

> The data is in output file, so I need to have at least one argument to read
> that file. Also I think read.table() needs the number of columns in all the
> rows to be same which is not true with .psl files.  The following output
> shows that:
>
> 1> dataTable = read.table('output.psl');
> Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings,
> :  line 1 did not have 25 elements
> In addition: Warning message:
> In read.table("output.psl") :
> incomplete final line found by readTableHeader on 'output.psl'
>
>
Hello, Fahim.

Please keep the replies on the list so you get the best help possible and
everyone can learn from the answers.  You really need to read the help for
read.table().  In particular, you will want to know what sep, skip, nlines,
and fill arguments do.

Sean




> Do you know any method through which I can read a block of lines in a
> file(say from line 50 to line 100). That will solve my case.
> ReadLines() function read the first n lines. For example.
> R>    x<-readLines(dataFile,n=6)
>
> 1> x
> [1] "psLayout version
> 3"
>
> [2]
> ""
>
> [3] "match\tmis- \trep. \tN's\tQ gap\tQ gap\tT gap\tT gap\tstrand\tQ
> \tQ   \tQ    \tQ  \tT        \tT   \tT    \tT  \tblock\tblockSizes
> \tqStarts\t tStarts"
> [4] "     \tmatch\tmatch\t   \tcount\tbases\tcount\tbases\t      \tname
> \tsize\tstart\tend\tname
> \tsize\tstart\tend\tcount"
> [5]
> "---------------------------------------------------------------------------------------------------------------------------------------------------------------"
> [6]
> "25\t0\t0\t0\t0\t0\t0\t0\t+\t1367452_atAAAAAABBBBBBBBB\t25\t0\t25\tchr11\t87759784\t81380087\t81380112\t1\t25,\t0,\t81380087,"
>
> 1>
>
>
> Thanks and regards.
> Fahim
>
>
>
>
> On Thu, May 13, 2010 at 12:15 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
>>
>>
>> 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
>>
>>
>
>
> --
> Mohammad Fahim
> Louisville, KY, USA
> Ph:  +1-502-409-1167
>

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