Re: [R-sig-phylo] reading nexus file from treebase?
Hi Mark, Brian and others, Mark Holder wrote on 25/03/2011 23:12: Hi all, Adding a command skipping feature to ape, might make it a good bit more robust to some of the weird files that are out there. I'm afraid that I'm not familiar enough with the code to suggest where those changes should go. It's done. I've also fixed a bug in write.nexus() at the same occasion. I've just submitted ape 2.7-1 to CRAN. For those who'd like to try it right now, I've updated svn and uploaded the sources here: http://ape.mpl.ird.fr/ape_2.7-1.tar.gz Cheers, Emmanuel The NEXUS standard indicates that parsers should skip commands that they don't understand. This can lead to problems (if there were multiple taxa blocks in the same file and you ignore the LINK commands, for instance). But in many cases, skipping these commands will work fine. Skipping a command simply entails reading NEXUS tokens until the token; is encountered. The tokenization rules are spec ( http://www.ncbi.nlm.nih.gov/pubmed/11975335 ). Mesquite also occasionally uses a BLOCKID command (in pretty much any block). all the best, Mark On Mar 25, 2011, at 10:58 AM, Brian O'Meara wrote: TITLE and LINK are used by Mesquite but not many other Nexus-reading programs (TITLE appears as a future reserved command name in the Maddison et al. (1997) nexus specification but I don't see LINK there). Brian ___ Brian O'Meara Assistant Professor Dept. of Ecology Evolutionary Biology U. of Tennessee, Knoxville http://www.brianomeara.info Students wanted: Applications due Dec. 15, annually Postdoc collaborators wanted: Check NIMBioS' website Funding wanted: Want to collaborate on a grant? On Fri, Mar 25, 2011 at 11:28 AM, Hilmar Lapp hl...@nescent.org wrote: Thanks for tracking this down, Emmanuel. I'm forwarding this to the TreeBASE developers list for consideration. BTW the phylobase implementation uses NCL (NEXUS Class Library, in C++) for parsing NEXUS. Given the difference, probably ape does not? -hilmar [-- cut --] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reading nexus file from treebase?
Thanks for tracking this down, Emmanuel. I'm forwarding this to the TreeBASE developers list for consideration. BTW the phylobase implementation uses NCL (NEXUS Class Library, in C+ +) for parsing NEXUS. Given the difference, probably ape does not? -hilmar On Mar 25, 2011, at 12:00 AM, Emmanuel Paradis wrote: Scott, readNexus (phylobase) can read your tree but not read.nexus (ape). The problem is the two lines inserted within the TREES block: BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] If you delete them, it's OK. FigTree also cannot read this file. Cheers, Emmanuel François Michonneau wrote on 25/03/2011 00:35: Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.com wrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- === : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : === ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
[R-sig-phylo] reading nexus file from treebase?
Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reading nexus file from treebase?
Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.comwrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] reading nexus file from treebase?
Scott, readNexus (phylobase) can read your tree but not read.nexus (ape). The problem is the two lines inserted within the TREES block: BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] If you delete them, it's OK. FigTree also cannot read this file. Cheers, Emmanuel François Michonneau wrote on 25/03/2011 00:35: Hi Scott, Which version of phylobase are you using and which architecture? I can read the file on my machine. Cheers, -- François On Thu, Mar 24, 2011 at 12:39, Scott Chamberlain myrmecocys...@gmail.comwrote: Hello, I can't get read.nexus (ape) or readNexus (phylobase) to read nexus files downloaded from treebase with URLs parsed from xml files. I can't manually edit each file as I want to read a lot of these files. Is there an easy fix? One of the files is copied below. Thanks! Scott Chamberlain Rice University, EEB Dept. #NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Downloaded on March 24, 2011; 16:32 GMT TreeBASE (cc) 1994-2008 Study reference: Brown R., Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165] BEGIN TAXA; TITLE M4787; DIMENSIONS NTAX=16; TAXLABELS Chalcides_coeruleopunctatus_E2806.20 Chalcides_coeruleopunctatus_E2806.22 Chalcides_manueli_E2506.1 Chalcides_mionecton_mionecton_E2506.10 Chalcides_mionecton_mionecton_E2506.12 Chalcides_mionecton_trifasciatus_E2506.18 Chalcides_polylepis_E14124.1 Chalcides_polylepis_E14124.2 Chalcides_polylepis_E2506.21 Chalcides_sexlineatus_bistriatus_E2806.6 Chalcides_sexlineatus_sexlineatus_E2806.8 Chalcides_simonyi_E3007.2 Chalcides_sphenopsiformis_E8121.26 Chalcides_sphenopsiformis_E8121.27 Chalcides_viridanus_E2806.10 Chalcides_viridanus_E2806.14 ; END; BEGIN TREES; TITLE Tb10793; LINK TAXA = M4787; TREE Fig._3c = [R] ((Chalcides_sphenopsiformis_E8121.26,Chalcides_sphenopsiformis_E8121.27),(((Chalcides_viridanus_E2806.10,Chalcides_viridanus_E2806.14),((Chalcides_sexlineatus_bistriatus_E2806.6,Chalcides_sexlineatus_sexlineatus_E2806.8),(Chalcides_coeruleopunctatus_E2806.22,Chalcides_coeruleopunctatus_E2806.20))),(Chalcides_simonyi_E3007.2,((Chalcides_mionecton_trifasciatus_E2506.18,(Chalcides_mionecton_mionecton_E2506.12,Chalcides_mionecton_mionecton_E2506.10)),(Chalcides_manueli_E2506.1,(Chalcides_polylepis_E14124.1,(Chalcides_polylepis_E14124.2,Chalcides_polylepis_E2506.21))); [! TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr6136] END; [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
