read gz compressed wig files?
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@hamid-bolouri-4572
Last seen 9.1 years ago
United States
Thanks Steve; > import.wig(gzopen('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.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.w ig.gz")) using gzfile instead of gzopen avoids the error message, but seems to produce an empty object > import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.wig.gz')) RangedDataList of length 0 > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IRanges_1.8.8 rtracklayer_1.10.6 RCurl_1.5-0.1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.2 BSgenome_1.18.3 GenomicRanges_1.2.3 tools_2.12.1 XML_3.2-0.2 > Thanks again. Hamid On Thu, Mar 31, 2011 at 12:04 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > 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/wgEncodeR egMarkEnhH3k27ac/ >> >> 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 > -- http://labs.fhcrc.org/bolouri
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@steve-lianoglou-2771
Last seen 15 months ago
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Hi, On Thu, Mar 31, 2011 at 7:03 PM, Hamid Bolouri <hbolouri at="" gmail.com=""> wrote: > Thanks Steve; > >> import.wig(gzopen('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562 H3k9me1.wig.gz')) > Error in import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_dat a\\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...\\wgEncodeBroadChipSeqSignalK562 H3k9me1.wig.gz')) > RangedDataList of length 0 If you unzip the file and read it in "as normal", does it work differently? -- 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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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...\\wgEncodeBroadChipSeqSignalK56 2H3k9me1.wig.gz')) >> Error in import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_da ta\\wgEncodeBroadChipSeqSignalK562H3k9me1.wig.gz")) >> : >> error in evaluating the argument 'con' in selecting a method for >> function 'import.wig' >> >>> traceback() >> 1: import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9me 1.wig.gz")) >> >> >> using gzfile instead of gzopen avoids the error message, but seems to >> produce an empty object >>> import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK56 2H3k9me1.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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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...\\wgEncodeBroadChipSeqSignalK5 62H3k9me1.wig.gz')) >>> >>> Error in >>> import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\wgEn codeBroadChipSeqSignalK562H3k9me1.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...\\wgEncodeBroadChipSeqSignalK5 62H3k9me1.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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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...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.wig.gz')) > >>> > >>> Error in > >>> > import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\wgEnco deBroadChipSeqSignalK562H3k9me1.wig.gz")) > >>> : > >>> error in evaluating the argument 'con' in selecting a method for > >>> function 'import.wig' > >>> > >>>> traceback() > >>> > >>> 1: > >>> > import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wi g.gz")) > >>> > >>> > >>> using gzfile instead of gzopen avoids the error message, but seems to > >>> produce an empty object > >>>> > >>>> > >>>> > import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.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 > [[alternative HTML version deleted]]
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Thanks for the suggestion Michael. FYI: doing import(x, format = "wigLines") on a ~220MB (unzipped) ENCODE wig file, R crashed after about an hour with the minimalist Unix (Ubuntu) message: 'Killed'. I am guessing a memory limit issue (which is what I get trying the same command on a Windows PC). Thanks Hamid FYI, sessionInfo for a restarted session: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.2 [4] GenomicRanges_1.2.1 IRanges_1.8.8 tools_2.12.0 [7] XML_3.2-0 On Fri, Apr 1, 2011 at 2:33 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > 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 at="" 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 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...\\wgEncodeBroadChipSeqSigna lK562H3k9me1.wig.gz')) >> >>> >> >>> Error in >> >>> >> >>> import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\w gEncodeBroadChipSeqSignalK562H3k9me1.wig.gz")) >> >>> : >> >>> ?error in evaluating the argument 'con' in selecting a method for >> >>> function 'import.wig' >> >>> >> >>>> traceback() >> >>> >> >>> 1: >> >>> >> >>> import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9m e1.wig.gz")) >> >>> >> >>> >> >>> using gzfile instead of gzopen avoids the error message, but seems to >> >>> produce an empty object >> >>>> >> >>>> >> >>>> >> >>>> import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSigna lK562H3k9me1.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 > > -- http://labs.fhcrc.org/bolouri
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On Fri, Apr 1, 2011 at 5:43 PM, Hamid Bolouri <hbolouri@gmail.com> wrote: > Thanks for the suggestion Michael. > > FYI: doing import(x, format = "wigLines") on a ~220MB (unzipped) > ENCODE wig file, R crashed after about an hour with the minimalist > Unix (Ubuntu) message: 'Killed'. I am guessing a memory limit issue > (which is what I get trying the same command on a Windows PC). > > Yep, just ran out of memory. A fixedStep WIG file like this will be 4X its file size in R as a RangedData/GRanges, so 1GB. Given that the parser is written in R and thus is making various copies of the data, it's going to take at least 4GB of memory to parse a file like this. I would recommend using bigWig import.bw) instead. That way, you can just read in the parts of the data that you need, and incremental processing becomes possible. This might be the bigWig you want: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroad Histone/wgEncodeBroadHistoneK562H3k9me1StdSig.bigWig > Thanks > > Hamid > FYI, sessionInfo for a restarted session: > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] rtracklayer_1.10.6 RCurl_1.4-3 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.2 > [4] GenomicRanges_1.2.1 IRanges_1.8.8 tools_2.12.0 > [7] XML_3.2-0 > > > On Fri, Apr 1, 2011 at 2:33 PM, Michael Lawrence > <lawrence.michael@gene.com> wrote: > > 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...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.wig.gz')) > >> >>> > >> >>> Error in > >> >>> > >> >>> > import.wig(gzopen("C:\\Users\\hbolouri\\Desktop\\ENCODE_data\\wgEnco deBroadChipSeqSignalK562H3k9me1.wig.gz")) > >> >>> : > >> >>> error in evaluating the argument 'con' in selecting a method for > >> >>> function 'import.wig' > >> >>> > >> >>>> traceback() > >> >>> > >> >>> 1: > >> >>> > >> >>> > import.wig(gzopen("C:\\...\\wgEncodeBroadChipSeqSignalK562H3k9me1.wi g.gz")) > >> >>> > >> >>> > >> >>> using gzfile instead of gzopen avoids the error message, but seems > to > >> >>> produce an empty object > >> >>>> > >> >>>> > >> >>>> > >> >>>> > import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSignalK562H 3k9me1.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 > > > > > > > > -- > http://labs.fhcrc.org/bolouri > [[alternative HTML version deleted]]
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Thanks very much Michael. I'll use bigWig where it's available, and process wig-only datasets using wigLines on large-memory nodes. AOK. Thanks to everyone for all the help. Hamid On Fri, Apr 1, 2011 at 9:18 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > > > On Fri, Apr 1, 2011 at 5:43 PM, Hamid Bolouri <hbolouri at="" gmail.com=""> wrote: >> >> Thanks for the suggestion Michael. >> >> FYI: doing ? import(x, format = "wigLines") ? ?on a ~220MB (unzipped) >> ENCODE wig file, R crashed after about an hour with the minimalist >> Unix (Ubuntu) message: 'Killed'. ?I am guessing a memory limit issue >> (which is what I get trying the same command on a Windows PC). >> > > Yep, just ran out of memory. A fixedStep WIG file like this will be 4X its > file size in R as a RangedData/GRanges, so 1GB. Given that the parser is > written in R and thus is making various copies of the data, it's going to > take at least 4GB of memory to parse a file like this. > > I would recommend using bigWig import.bw) instead. That way, you can just > read in the parts of the data that you need, and incremental processing > becomes possible. > > This might be the bigWig you want: > > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBro adHistone/wgEncodeBroadHistoneK562H3k9me1StdSig.bigWig > > >> >> Thanks >> >> Hamid >> FYI, sessionInfo for a restarted session: >> > sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> ?[1] LC_CTYPE=en_US.UTF-8 ? ? ? LC_NUMERIC=C >> ?[3] LC_TIME=en_US.UTF-8 ? ? ? ?LC_COLLATE=en_US.UTF-8 >> ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_US.UTF-8 >> ?[7] LC_PAPER=en_US.UTF-8 ? ? ? LC_NAME=C >> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] rtracklayer_1.10.6 RCurl_1.4-3 ? ? ? ?bitops_1.0-4.1 >> >> loaded via a namespace (and not attached): >> [1] Biobase_2.10.0 ? ? ?Biostrings_2.18.0 ? BSgenome_1.18.2 >> [4] GenomicRanges_1.2.1 IRanges_1.8.8 ? ? ? tools_2.12.0 >> [7] XML_3.2-0 >> >> >> On Fri, Apr 1, 2011 at 2:33 PM, Michael Lawrence >> <lawrence.michael at="" gene.com=""> wrote: >> > 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 at="" 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 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...\\wgEncodeBroadChipSeqSi gnalK562H3k9me1.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:\\...\\wgEncodeBroadChipSeqSignalK562H3 k9me1.wig.gz")) >> >> >>> >> >> >>> >> >> >>> using gzfile instead of gzopen avoids the error message, but seems >> >> >>> to >> >> >>> produce an empty object >> >> >>>> >> >> >>>> >> >> >>>> >> >> >>>> >> >> >>>> import.wig(gzfile('C:\\...pathto...\\wgEncodeBroadChipSeqSi gnalK562H3k9me1.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 >> > >> > >> >> >> >> -- >> http://labs.fhcrc.org/bolouri > > -- http://labs.fhcrc.org/bolouri
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