Btw, rtracklayer has an internal function, import.wigLines() that can parse
the lines after the track line. Could try using that.  Can use import(x,
format = "wigLines") to get there.

On Fri, Apr 1, 2011 at 1:25 PM, Hamid Bolouri <hbolouri@gmail.com> wrote:

> Martin, Steve; Thank you both much.
>
> Pretty amazing that hundreds of ENCODE data files mayt be
> 'non-standard'. Lesson learnt.
>
> Thanks again,
>
> Hamid
>
> On Fri, Apr 1, 2011 at 12:21 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:
> > On 04/01/2011 08:29 AM, Steve Lianoglou wrote:
> >>
> >> Hi,
> >>
> >> On Thu, Mar 31, 2011 at 7:03 PM, Hamid Bolouri<hbolouri@gmail.com>
>  wrote:
> >>>
> >>> Thanks Steve;
> >>>
> >>>>
> >>>>
> import.wig(gzopen('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz'))
> >>>
> >>> Error in
> >>>
> import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz"))
> >>> :
> >>>  error in evaluating the argument 'con' in selecting a method for
> >>> function 'import.wig'
> >>>
> >>>> traceback()
> >>>
> >>> 1:
> >>>
> import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz"))
> >>>
> >>>
> >>> using gzfile instead of gzopen avoids the error message, but seems to
> >>> produce an empty object
> >>>>
> >>>>
> >>>>
> import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz'))
> >>>
> >>> RangedDataList of length 0
> >>
> >> If you unzip the file and read it in "as normal", does it work
> >> differently?
> >
> > I think the basic problem is that these files are not strictly wiggle,
> > missing an initial 'track' line:
> >
> >> head wgEncodeBroadChipSeqSignalHepg2H3k27ac.wig
> > fixedStep chrom=chr1 start=1 step=25
> > 113
> > 136
> >
> > Martin
> >
> >>
> >
> >
> > --
> > Computational Biology
> > Fred Hutchinson Cancer Research Center
> > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
> >
> > Location: M1-B861
> > Telephone: 206 667-2793
> >
>
>
>
> --
> http://labs.fhcrc.org/bolouri
>

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