[BioC] read gz compressed wig files?

[Martin Morgan]

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

>


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