[BioC] read gz compressed wig files?

[Hamid Bolouri]

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 at 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 at 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
>



-- 
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