[med-svn] [python-dendropy] 01/01: Add separate sumtrees package including manpage
Andreas Tille
tille at debian.org
Mon Jun 29 07:42:26 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-dendropy.
commit 28625a7f51d3475c8ee0212d20949b27d97a8d52
Author: Andreas Tille <tille at 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
--
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