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commit 28625a7f51d3475c8ee0212d20949b27d97a8d52 Author: Andreas Tille <ti...@debian.org> Date: Mon Jun 29 09:42:05 2015 +0200 Add separate sumtrees package including manpage --- debian/control | 40 +++--- debian/rules | 8 +- debian/sumtrees.1 | 351 +++++++++++++++++++++++++++++++++++++++++++++++ debian/sumtrees.manpages | 1 + 4 files changed, 378 insertions(+), 22 deletions(-) diff --git a/debian/control b/debian/control index e5f6be9..1cfe9aa 100644 --- a/debian/control +++ b/debian/control @@ -8,8 +8,7 @@ Build-Depends: debhelper (>= 9), python-all, python-setuptools, python3-all, - python3-setuptools, - python-sphinx + python3-setuptools Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-dendropy.git Vcs-Git: git://anonscm.debian.org/debian-med/python-dendropy.git @@ -55,24 +54,25 @@ Description: DendroPy Phylogenetic Computing Library (Python 3) . This package provides python3 modules. -Package: python-dendropy-doc +Package: sumtrees Architecture: all -Section: doc -Depends: ${misc:Depends}, - ${sphinxdoc:Depends}, - libjs-mathjax -Description: DendroPy Phylogenetic Computing Library (Dokumentation) - DendroPy is a Python library for phylogenetic computing. It provides - classes and functions for the simulation, processing, and manipulation - of phylogenetic trees and character matrices, and supports the reading - and writing of phylogenetic data in a range of formats, such as NEXUS, - NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing - some useful phylogenetic operations, such as data conversion and tree - posterior distribution summarization, are also distributed and installed - as part of the library. DendroPy can thus function as a stand-alone - library for phylogenetics, a component of more complex multi-library - phyloinformatic pipelines, or as a scripting “glue” that assembles and - drives such pipelines. +Depends: ${shlibs:Depends}, + ${misc:Depends}, + ${python3:Depends}, + python3-dendropy +Description: Phylogenetic Tree Summarization and Annotation + SumTrees is a program to summarize non-parameteric bootstrap or + Bayesian posterior probability support for splits or clades on + phylogenetic trees. . - This package provides modules documentation. + The basis of the support assessment is typically given by a set of + non-parametric bootstrap replicate tree samples produced by programs + such as GARLI or RAxML, or by a set of MCMC tree samples produced by + programs such as Mr. Bayes or BEAST. The proportion of trees out of the + samples in which a particular split is found is taken to be the degree + of support for that split as indicated by the samples. The samples that + are the basis of the support can be distributed across multiple files, + and a burn-in option allows for an initial number of trees in each file + to be excluded from the analysis if they are not considered to be drawn + from the true support distribution. diff --git a/debian/rules b/debian/rules index eea0d86..1736f77 100755 --- a/debian/rules +++ b/debian/rules @@ -5,10 +5,12 @@ DH_VERBOSE := 1 DEBPKGNAME:=$(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') docpkg:=$(DEBPKGNAME)-doc +SUMTREES:=sumtrees + export PYBUILD_NAME=dendropy %: - dh $@ --with python2,python3,sphinxdoc --buildsystem=pybuild + dh $@ --with python2,python3 --buildsystem=pybuild override_dh_auto_test: ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS))) @@ -23,4 +25,6 @@ endif override_dh_install: dh_install ## FIXME: This needs to be clarified with python modules team - mv debian/python3-$(PYBUILD_NAME)/usr/bin/sumtrees.py debian/python3-$(PYBUILD_NAME)/usr/bin/sumtrees3.py + mkdir -p debian/$(SUMTREES)/usr/bin + mv debian/python3-$(PYBUILD_NAME)/usr/bin/sumtrees.py debian/$(SUMTREES)/usr/bin/sumtrees + rm -rf debian/python-$(PYBUILD_NAME)/usr/bin diff --git a/debian/sumtrees.1 b/debian/sumtrees.1 new file mode 100644 index 0000000..c0a9cf6 --- /dev/null +++ b/debian/sumtrees.1 @@ -0,0 +1,351 @@ +.TH SUMTREES "1" "June 2015" "sumtrees 4.0.2" "User Commands" +.SH NAME +sumtrees \- Phylogenetic Tree Summarization and Annotation +.SH SYNOPSIS +.B sumtrees +\fI[\-i FORMAT] [\-b BURNIN] [\-\-force\-rooted] [\-\-force\-unrooted]\fR +.SH DESCRIPTION +SumTrees is a program to summarize non-parameteric bootstrap or +Bayesian posterior probability support for splits or clades on +phylogenetic trees. +.P +The basis of the support assessment is typically given by a set of +non-parametric bootstrap replicate tree samples produced by programs +such as GARLI or RAxML, or by a set of MCMC tree samples produced by +programs such as Mr. Bayes or BEAST. The proportion of trees out of the +samples in which a particular split is found is taken to be the degree +of support for that split as indicated by the samples. The samples that +are the basis of the support can be distributed across multiple files, +and a burn-in option allows for an initial number of trees in each file +to be excluded from the analysis if they are not considered to be drawn +from the true support distribution. +.P +Summarizations collections of trees, e.g., MCMC samples from a posterior +distribution, non\-parametric bootstrap replicates, mapping posterior +probability, support, or frequency that splits/clades are found in the source +set of trees onto a target tree. +.SH OPTIONS +.SS "Source Options:" +.TP +TREE\-FILEPATH +Source(s) of trees to summarize. At least one valid +source of trees must be provided. Use '\-' to specify +reading from standard input (note that this requires +the input file format to be explicitly set using the +\&'\-\-source\-format' option). +.TP +\fB\-i\fR FORMAT, \fB\-\-input\-format\fR FORMAT, \fB\-\-source\-format\fR FORMAT +Format of all input trees (defaults to handling either +NEXUS or NEWICK through inspection; it is more +efficient to explicitly specify the format if it is +known). +.TP +\fB\-b\fR BURNIN, \fB\-\-burnin\fR BURNIN +Number of trees to skip from the beginning of *each* +tree file when counting support (default: 0). +.TP +\fB\-\-force\-rooted\fR, \fB\-\-rooted\fR +Treat source trees as rooted. +.TP +\fB\-\-force\-unrooted\fR, \fB\-\-unrooted\fR +Treat source trees as unrooted. +.TP +\fB\-v\fR, \fB\-\-ultrametricity\-precision\fR, \fB\-\-branch\-length\-epsilon\fR +Precision to use when validating ultrametricity +(default: 1e\-05; specify '0' to disable validation). +.TP +\fB\-\-weighted\-trees\fR +Use weights of trees (as indicated by '[&W m/n]' +comment token) to weight contribution of splits found +on each tree to overall split frequencies. +.TP +\fB\-\-preserve\-underscores\fR +Do not convert unprotected (unquoted) underscores to +spaces when reading NEXUS/NEWICK format trees. +.TP +\fB\-\-taxon\-name\-filepath\fR FILEPATH +Path to file listing all the taxon names or labels +that will be found across the entire set of source +trees. This file should be a plain text file with a +single name list on each line. This file is only read +when multiprocessing ('\-M' or '\-m') is requested. When +multiprocessing using the '\-M' or '\-m' options, all +taxon names need to be defined in advance of any +actual tree analysis. By default this is done by +reading the first tree in the first tree source and +extracting the taxon names. At best, this is, +inefficient, as it involves an extraneous reading of +the tree. At worst, this can be errorneous, if the +first tree does not contain all the taxa. Explicitly +providing the taxon names via this option can avoid +these issues. +.SS "Target Tree Topology Options:" +.TP +\fB\-t\fR FILE, \fB\-\-target\-tree\-filepath\fR FILE +Summarize support and other information from the +source trees to topology or topologies given by the +tree(s) described in FILE. If no use\-specified target +topologies are given, then a summary topology will be +used as the target. Use the '\-s' or '\-\-summary\-target' +to specify the type of summary tree to use. +.TP +\fB\-s\fR SUMMARY\-TYPE, \fB\-\-summary\-target\fR SUMMARY\-TYPE +Construct and summarize support and other information +from the source trees to one of the following summary +topologies: +\- 'consensus' +.TP +A consensus tree. The minimum frequency +threshold of clades to be included can be +specified using the '\-f' or '\-\-min\-clade\-freq' +flags. This is the DEFAULT if a user\- specified +target tree is not given through the '\-t' or +\&'\-\-target\-tree\-filepath' options. +.TP +\- 'mcct' +The maximum clade credibility tree. The tree +from the source set that maximizes the *product* +of clade posterior probabilities. +.TP +\- 'msct' +The maximum clade credibility tree. The tree +from the source set that maximizes the *product* +of clade posterior probabilities. +.SS "Target Tree Supplemental Options:" +.TP +\fB\-f\fR #.##, \fB\-\-min\-consensus\-freq\fR #.##, \fB\-\-min\-freq\fR #.##, \fB\-\-min\-clade\-freq\fR #.## +If using a consensus tree summarization strategy, then +this is the minimum frequency or probability for a +clade or a split to be included in the resulting tree +(default: > 0.5). +.TP +\fB\-\-allow\-unknown\-target\-tree\-taxa\fR +Do not fail with error if target tree(s) have taxa not +previously encountered in source trees or defined in +the taxon discovery file. +.SS "Target Tree Rooting Options:" +.TP +\fB\-\-root\-target\-at\-outgroup\fR TAXON\-LABEL +Root target tree(s) using specified taxon as outgroup. +.TP +\fB\-\-root\-target\-at\-midpoint\fR +Root target tree(s) at midpoint. +.TP +\fB\-\-set\-outgroup\fR TAXON\-LABEL +Rotate the target trees such the specified taxon is in +the outgroup position, but do not explicitly change +the target tree rooting. +.SS "Target Tree Edge Options:" +.TP +\fB\-e\fR STRATEGY, \fB\-\-set\-edges\fR STRATEGY, \fB\-\-edges\fR STRATEGY +Set the edge lengths of the target or summary trees +based on the specified summarization STRATEGY: +\- 'mean\-length' +.TP +Edge lengths will be set to the mean of the +lengths of the corresponding split or clade in +the source trees. +.TP +\- 'median\-length' +Edge lengths will be set to the median of the +.TP +lengths of the corresponding split or clade in +the source trees. +.TP +\- 'mean\-age' +Edge lengths will be adjusted so that the age of +subtended nodes will be equal to the mean age of +the corresponding split or clade in the source +trees. Source trees will need to to be +ultrametric for this option. +.TP +\- 'median\-age' +Edge lengths will be adjusted so that the age of +subtended nodes will be equal to the median age +of the corresponding split or clade in the +source trees. Source trees will need to to be +ultrametric for this option. +.TP +\- support +Edge lengths will be set to the support value +for the split represented by the edge. +.TP +\- 'keep' +Do not change the existing edge lengths. This is +the DEFAULT if target tree(s) are sourced from +an external file using the '\-t' or '\-\-targettree\-filepath' option +.TP +\- 'clear' +Edge lengths will be cleared from the target +trees if they are present. +.TP +Note the default settings varies according to the +following, in order of preference: +(1) If target trees are specified using the '\-t' or +.TP +\&'\-\-target\-tree\-filepath' option, then the default edge +summarization strategy is: 'keep'. +.TP +(2) If target trees are not specified, but the +\&'\-\-summarize\-node\-ages' option is specified, +then the default edge summarization strategy is: +\&'mean\-age'. +.TP +(3) If no target trees are specified and the +node ages are NOT specified to be summarized, +then the default edge summarization strategy is: +\&'mean\-length'. +.TP +\fB\-\-force\-minimum\-edge\-length\fR FORCE_MINIMUM_EDGE_LENGTH +(If setting edge lengths) force all edges to be at +least this length. +.TP +\fB\-\-collapse\-negative\-edges\fR +(If setting edge lengths) force parent node ages to be +at least as old as its oldest child when summarizing +node ages. +.SS "Target Tree Annotation Options:" +.TP +\fB\-\-summarize\-node\-ages\fR, \fB\-\-ultrametric\fR, \fB\-\-node\-ages\fR +Assume that source trees are ultrametic and summarize +node ages (distances from tips). +.TP +\fB\-l\fR {support,keep,clear}, \fB\-\-labels\fR {support,keep,clear} +Set the node labels of the summary or target tree(s): +\- 'support' +.TP +Node labels will be set to the support value for +the clade represented by the node. This is the +DEFAULT. +.TP +\- 'keep' +Do not change the existing node labels. +.TP +\- 'clear' +Node labels will be cleared from the target +trees if they are present. +.TP +\fB\-\-suppress\-annotations\fR, \fB\-\-no\-annotations\fR +Do NOT annotate nodes and edges with any summarization +information metadata such as.support values, edge +length and/or node age summary statistcs, etc. +.SS "Support Expression Options:" +.TP +\fB\-p\fR, \fB\-\-percentages\fR +Indicate branch support as percentages (otherwise, +will report as proportions by default). +.TP +\fB\-d\fR #, \fB\-\-decimals\fR # +Number of decimal places in indication of support +values (default: 8). +.SS "Output Options:" +.TP +\fB\-o\fR FILEPATH, \fB\-\-output\-tree\-filepath\fR FILEPATH, \fB\-\-output\fR FILEPATH +Path to output file (if not specified, will print to +standard output). +.TP +\fB\-F\fR {nexus,newick,phylip,nexml}, \fB\-\-output\-tree\-format\fR {nexus,newick,phylip,nexml} +Format of the output tree file (if not specifed, +defaults to input format, if this has been explicitly +specified, or 'nexus' otherwise). +.TP +\fB\-x\fR PREFIX, \fB\-\-extended\-output\fR PREFIX +If specified, extended summarization information will +be generated, consisting of the following files: +\- '<PREFIX>.topologies.trees' +.TP +A collection of topologies found in the sources +reported with their associated posterior +probabilities as metadata annotations. +.TP +\- '<PREFIX>.bipartitions.trees' +A collection of bipartitions, each represented +as a tree, with associated information as +metadataannotations. +.TP +\- '<PREFIX>.bipartitions.tsv' +Table listing bipartitions as a group pattern as +the key column, and information regarding each +the bipartitions as the remaining columns. +.TP +\- '<PREFIX>.edge\-lengths.tsv' +List of bipartitions and corresponding edge +lengths. Only generated if edge lengths are +summarized. +.TP +\- '<PREFIX>.node\-ages.tsv' +List of bipartitions and corresponding ages. +Only generated if node ages are summarized. +.TP +\fB\-\-no\-taxa\-block\fR +When writing NEXUS format output, do not include a +taxa block in the output treefile (otherwise will +create taxa block by default). +.TP +\fB\-\-no\-analysis\-metainformation\fR, \fB\-\-no\-meta\-comments\fR +Do not include meta\-information describing the +summarization parameters and execution details. +.TP +\fB\-c\fR ADDITIONAL_COMMENTS, \fB\-\-additional\-comments\fR ADDITIONAL_COMMENTS +Additional comments to be added to the summary file. +.TP +\fB\-r\fR, \fB\-\-replace\fR +Replace/overwrite output file without asking if it +already exists. +.SS "Parallel Processing Options:" +.TP +\fB\-M\fR, \fB\-\-maximum\-multiprocessing\fR +Run in parallel mode using as many processors as +available, up to the number of sources. +.TP +\fB\-m\fR NUM\-PROCESSES, \fB\-\-multiprocessing\fR NUM\-PROCESSES +Run in parallel mode with up to a maximum of NUMPROCESSES processes ('max' or '#' means to run in as +many processes as there are cores on the local +machine; i.e., same as specifying '\-M' or '\-\-maximummultiprocessing'). +.SS "Program Logging Options:" +.TP +\fB\-g\fR LOG\-FREQUENCY, \fB\-\-log\-frequency\fR LOG\-FREQUENCY +Tree processing progress logging frequency (default: +500; set to 0 to suppress). +.TP +\fB\-q\fR, \fB\-\-quiet\fR +Suppress ALL logging, progress and feedback messages. +.SS "Program Error Options:" +.TP +\fB\-\-ignore\-missing\-support\fR +Ignore missing support tree files (note that at least +one must exist). +.SS "Program Information Options:" +.TP +\fB\-h\fR, \fB\-\-help\fR +Show help information for program and exit. +.TP +\fB\-\-citation\fR +Show citation information for program and exit. +.TP +\fB\-\-usage\-examples\fR +Show usage examples of program and exit. +.TP +\fB\-\-describe\fR +Show information regarding your DendroPy and Python +installations and exit. +.SH AUTHORS +Jeet Sukumaran and Mark T. Holder +.SH SEE ALSO +If any stage of your work or analyses relies on code or programs from +this library, either directly or indirectly (e.g., through usage of your +own or third\-party programs, pipelines, or toolkits which use, rely on, +incorporate, or are otherwise primarily derivative of code/programs in +this library), please cite: +.IP +Sukumaran, J and MT Holder. 2010. DendroPy: a Python library for +phylogenetic computing. Bioinformatics 26: 1569\-1571. +.IP +Sukumaran, J and MT Holder. SumTrees: Phylogenetic Tree Summarization. +4.0.0 (Jan 31 2015). Available at +https://github.com/jeetsukumaran/DendroPy. +.P +Note that, in the interests of scientific reproducibility, you should +describe in the text of your publications not only the specific +version of the SumTrees program, but also the DendroPy library used in +your analysis. For your information, you are running DendroPy 4.0.2. diff --git a/debian/sumtrees.manpages b/debian/sumtrees.manpages new file mode 100644 index 0000000..0f65186 --- /dev/null +++ b/debian/sumtrees.manpages @@ -0,0 +1 @@ +debian/*.1 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-dendropy.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit