readAligned input failed?

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ANYOU WANG ▴ 30

@anyou-wang-4388

Last seen 9.6 years ago

Hello, everyone A question about readAligned. I tried to input the .map aligned sequence data using readAligned, but it failed (detail below), even using the testing data downloaded from the ShortRead website. Could anyone give some suggestions? Thanks. Anyou expdir<-"/disk2/lab/tmp1/" Test.me3 <- sapply( list.files( expdir, "*.map" ),function(filename) readAligned(expdir, filename, type="MAQMapShort" )) Error: Input/Output 'readAligned' failed to parse files dirPath: '/disk2/lab/tmp1/' pattern: 'run4_lane8.map' type: 'MAQMapShort' error: function '_new_RoSeqs_from_CharAEAE' not provided by package 'Biostrings' ***my system info below Mandriva Linux 2010, 64bit, 8 CPU,12G RAM. [[alternative HTML version deleted]]

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ADD COMMENT • link 13.4 years ago ANYOU WANG ▴ 30

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Martin Morgan 25k

@martin-morgan-1513

Last seen 3 days ago

United States

On 12/13/2010 09:24 AM, ANYOU WANG wrote: > Hello, everyone > > A question about readAligned. I tried to input the .map > aligned sequence data using readAligned, but it failed (detail > below), even using the testing data downloaded from the ShortRead website. > Could anyone give some suggestions? Thanks. > > Anyou > > expdir<-"/disk2/lab/tmp1/" > Test.me3 <- sapply( list.files( expdir, "*.map" ),function(filename) > readAligned(expdir, filename, type="MAQMapShort" )) > > Error: Input/Output > > 'readAligned' failed to parse files > > dirPath: '/disk2/lab/tmp1/' > > pattern: 'run4_lane8.map' > > type: 'MAQMapShort' > > error: function '_new_RoSeqs_from_CharAEAE' not provided by > package 'Biostrings' Hi This suggests an incorrect version of Biostrings. Follow the directions here http://bioconductor.org/install/index.html#update-bioconductor- packages to update packages, and please let us know how it goes -- use sessionInfo() to report your session information Best, Martin > > > ***my system info below > > Mandriva Linux 2010, 64bit, 8 CPU,12G RAM. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793

ADD COMMENT • link 13.4 years ago Martin Morgan 25k

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Hi, Martin It is working after updated packages following your suggestion. Thanks. Best, Anyou On Mon, Dec 13, 2010 at 9:37 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 12/13/2010 09:24 AM, ANYOU WANG wrote: > > Hello, everyone > > > > A question about readAligned. I tried to input the .map > > aligned sequence data using readAligned, but it failed (detail > > below), even using the testing data downloaded from the ShortRead > website. > > Could anyone give some suggestions? Thanks. > > > > Anyou > > > > expdir<-"/disk2/lab/tmp1/" > > Test.me3 <- sapply( list.files( expdir, "*.map" ),function(filename) > > readAligned(expdir, filename, type="MAQMapShort" )) > > > > Error: Input/Output > > > > 'readAligned' failed to parse files > > > > dirPath: '/disk2/lab/tmp1/' > > > > pattern: 'run4_lane8.map' > > > > type: 'MAQMapShort' > > > > error: function '_new_RoSeqs_from_CharAEAE' not provided by > > package 'Biostrings' > > Hi > > This suggests an incorrect version of Biostrings. Follow the directions > here > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > to update packages, and please let us know how it goes -- use > sessionInfo() to report your session information > > Best, > > Martin > > > > > > ***my system info below > > > > Mandriva Linux 2010, 64bit, 8 CPU,12G RAM. > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]

ADD REPLY • link 13.4 years ago ANYOU WANG ▴ 30

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ANYOU WANG ▴ 30

@anyou-wang-4388

Last seen 9.6 years ago

Hello, everyone I forgot the sessionInfo() in my former post about the failure of readAligned. Here I reposted below it with this info. Thanks. Anyou A question about readAligned. I tried to input the .map aligned sequence data using readAligned, but it failed (detail below), even using the testing data downloaded from the ShortRead website. Could anyone give some suggestions? Thanks. Anyou expdir<-"/disk2/lab/tmp1/" Test.me3 <- sapply( list.files( expdir, "*.map" ),function(filename) readAligned(expdir, filename, type="MAQMapShort" )) Error: Input/Output 'readAligned' failed to parse files dirPath: '/disk2/lab/tmp1/' pattern: 'run4_lane8.map' type: 'MAQMapShort' error: function '_new_RoSeqs_from_CharAEAE' not provided by package 'Biostrings' > 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] ShortRead_1.4.0 lattice_0.19-13 BSgenome_1.14.2 Biostrings_2.18.2 [5] IRanges_1.8.2 loaded via a namespace (and not attached): [1] Biobase_2.10.0 grid_2.12.0 hwriter_1.2 [[alternative HTML version deleted]]

ADD COMMENT • link 13.4 years ago ANYOU WANG ▴ 30

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