read gz compressed wig files?
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@hamid-bolouri-4572
Last seen 9.1 years ago
United States
hi; Is there a way to read gz compressed wiggle files (.wig.gz) without decompressing them first? I couldn't find anything online. Example files: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeRegMa rkEnhH3k27ac/ Thanks Hamid Bolouri -- http://labs.fhcrc.org/bolouri
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@steve-lianoglou-2771
Last seen 15 months ago
United States
Hi, On Mon, Mar 28, 2011 at 5:32 PM, Hamid Bolouri <hbolouri at="" gmail.com=""> wrote: > hi; Is there a way to read gz compressed wiggle files (.wig.gz) > without decompressing them first? I couldn't find anything online. > > Example files: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeReg MarkEnhH3k27ac/ Maybe the import.wig (or import.bw if you've got bigwig files). That function take in a `con` (connection) object, perhaps you can make a "connection" to your wig.gz file via `gzopen()` and pass the result into the import.wig, ie: R> import.wig(gzopen('/path/to/*.wig.gz')) I actually haven't tried it, but I reckon it could work. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Sorry, forgot to add that these import.wig and import.bw are in the rtracklayer package. On Thu, Mar 31, 2011 at 3:04 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Mon, Mar 28, 2011 at 5:32 PM, Hamid Bolouri <hbolouri at="" gmail.com=""> wrote: >> hi; Is there a way to read gz compressed wiggle files (.wig.gz) >> without decompressing them first? I couldn't find anything online. >> >> Example files: >> >> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeRe gMarkEnhH3k27ac/ > > Maybe the import.wig (or import.bw if you've got bigwig files). > > That function take in a `con` (connection) object, perhaps you can > make a "connection" to your wig.gz file via `gzopen()` and pass the > result into the import.wig, ie: > > R> import.wig(gzopen('/path/to/*.wig.gz')) > > I actually haven't tried it, but I reckon it could work. > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| Memorial Sloan-Kettering Cancer Center > ?| Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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