Merge pull request #164 from McTavishLab/clean-docs

Clean docs
McTavishLab · Aug 11, 2021 · 2fe3aed · 2fe3aed
2 parents 4f8543f + 341d2c5
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diff --git a/.gitignore b/.gitignore
@@ -13,6 +13,8 @@ tests/data/precooked/*
 docs/example_scripts/output/*
 tests/data/tmp/*
 tests/debugging/*
+tests/tmp
+tests/fromfile
 .Rproj.user
 *Rproj
 *Rhistory

diff --git a/README.Rmd b/README.Rmd
@@ -14,9 +14,9 @@ knitr::opts_chunk$set(
 IS_README <- TRUE
 ```
 
-<img align="left" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/cleanup/docs/physcraper-long.png">
+<img align="left" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
 
-# Physcraper
+# Welcome to Physcraper’s repository!
 
 [![Build Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://travis-ci.org/McTavishLab/physcraper)[![Documentation](https://readthedocs.org/projects/physcraper/badge/?version=latest&style=flat)](https://physcraper.readthedocs.io/en/latest/)[![codecov](https://codecov.io/gh/McTavishLab/physcraper/branch/main/graph/badge.svg)](https://codecov.io/gh/McTavishLab/physcraper)
 
@@ -26,38 +26,44 @@ IS_README <- TRUE
 <p></p>
 
 
-## Automated gene tree updating!
-
-
 ```{r child="docs/mds/intro.md"}
 
 ```
 
+You are now on the code repository. Please refer to Physcraper’s
+[documentation website](https://physcraper.readthedocs.io/en/latest/)
+for more details on:
 
-This is the code repository.
-Please refer to Physcraper's [documentation website](https://physcraper.readthedocs.io/en/latest/) for more details
-on [installation](https://physcraper.readthedocs.io/en/latest/install.html) instructions
-using an Anaconda or a Virtualenv Python virtual environment,
-[function](https://physcraper.readthedocs.io/en/latest/apidocs.html) usage,
-tutorials on finding and choosing a [starting dataset](https://physcraper.readthedocs.io/en/latest/find_trees.html),
-[running](https://physcraper.readthedocs.io/en/latest/physcraper_run.html) a full analysis,
-and [visualizing and analysing](https://physcraper.readthedocs.io/en/latest/data_exploration.html) results,
-as well as real life [examples](https://physcraper.readthedocs.io/en/latest/examples.html)
-and tools for [developers](https://physcraper.readthedocs.io/en/latest/CONTRIBUTING.html).
-
+- [installation](https://physcraper.readthedocs.io/en/latest/install.html)
+instructions using an Anaconda or a Virtualenv Python virtual
+environment,
+- [function](https://physcraper.readthedocs.io/en/latest/apidocs.html)
+usage,
+- finding and choosing a [starting dataset](https://physcraper.readthedocs.io/en/latest/find-trees.html),
+- [running](https://physcraper.readthedocs.io/en/latest/run.html) a full analysis,
+- [visualizing and analysing](https://physcraper.readthedocs.io/en/latest/results.html) results,
+- real life [examples](https://physcraper.readthedocs.io/en/latest/examples.html), and
+- tools for [developers](https://physcraper.readthedocs.io/en/latest/CONTRIBUTING.html).
 
 
 :hamster: :palm_tree: :frog: :ear_of_rice: :panda_face: :tulip: :octopus: :blossom: :whale: :mushroom: :ant: :cactus: :fish: :maple_leaf: :water_buffalo: 🦠 :shell: :bug: :octocat:
 
 
-```{r child="docs/mds/intro-dendropy.md"}
+```{r child="docs/mds/citation.md"}
 
 ```
 
-```{r child="docs/mds/citation.md"}
+
+```{r child="docs/mds/license.md"}
 
 ```
 
-```{r child="docs/mds/license.md"}
+
+```{r child="docs/mds/contact.md"}
+
+```
+
+
+```{r child="docs/mds/intro-requirements.md"}
 
 ```
diff --git a/README.md b/README.md
@@ -1,9 +1,9 @@
 
 <!-- README.md is generated from README.Rmd; please edit the .Rmd file and then from R do rmarkdown::render("README.Rmd")-->
 
-<img align="left" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/master/docs/physcraper-long.png">
+<img align="left" width="250" src="https://raw.githubusercontent.com/McTavishLab/physcraper/main/docs/physcraper-long.png">
 
-# Physcraper
+# Welcome to Physcraper’s repository\!
 
 [![Build
 Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://travis-ci.org/McTavishLab/physcraper)[![Documentation](https://readthedocs.org/projects/physcraper/badge/?version=latest&style=flat)](https://physcraper.readthedocs.io/en/latest/)[![codecov](https://codecov.io/gh/McTavishLab/physcraper/branch/main/graph/badge.svg)](https://codecov.io/gh/McTavishLab/physcraper)
@@ -16,66 +16,148 @@ Status](https://travis-ci.org/McTavishLab/physcraper.svg?branch=main)](https://t
 
 </p>
 
-## Automated gene tree updating\!
-
-Use a tree and a single locus alignment to find and add homologous
-sequences to improve and advance phylogenetic inference in a group.
-
-The tool is under active development in the [McTavish
-Lab](https://mctavishlab.github.io/). Please post a GitHub issue
-[here](https://github.com/McTavishLab/physcraper/issues) or contact
-<ejmctavish@ucmerced.edu> if you need any help or have feedback.
-
-This is the code repository. Please refer to Physcraper’s
+## Automated gene tree updating <br> with the Open Tree of Life
+
+Use a phylogenetic tree and a DNA alignment to automatically find and
+add nucleotide sequences from a genetic database, to reproducibly
+improve and advance phylogenetic knowledge within a biological group.
+
+Physcraper relies on
+[taxonomic](https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3)
+and [phylogenetic](https://github.com/OpenTreeOfLife/phylesystem-1)
+resources and [programmatic
+tools](https://github.com/OpenTreeOfLife/germinator/wiki/Open-Tree-of-Life-Web-APIs)
+from the [Open Tree of
+Life](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302)
+project.
+
+Physcraper also leverages on programmatic tools from the
+[TreeBASE](https://treebase.org/treebase-web/urlAPI.html) project and
+[NCBI](https://www.ncbi.nlm.nih.gov/home/develop/api/), as well as
+multiple software projects listed as [requirements](#Requirements)
+below, to create an automatic and reproducible workflow for
+phylogenetics.
+
+You are now on the code repository. Please refer to Physcraper’s
 [documentation website](https://physcraper.readthedocs.io/en/latest/)
-for more details on
-[installation](https://physcraper.readthedocs.io/en/latest/install.html)
-instructions using an Anaconda or a Virtualenv Python virtual
-environment,
-[function](https://physcraper.readthedocs.io/en/latest/apidocs.html)
-usage, tutorials on finding and choosing a [starting
-dataset](https://physcraper.readthedocs.io/en/latest/find_trees.html),
-[running](https://physcraper.readthedocs.io/en/latest/physcraper_run.html)
-a full analysis, and [visualizing and
-analysing](https://physcraper.readthedocs.io/en/latest/data_exploration.html)
-results, as well as real life
-[examples](https://physcraper.readthedocs.io/en/latest/examples.html)
-and tools for
-[developers](https://physcraper.readthedocs.io/en/latest/CONTRIBUTING.html).
+for more details
+    on:
+
+  - [installation](https://physcraper.readthedocs.io/en/latest/install.html)
+    instructions using an Anaconda or a Virtualenv Python virtual
+    environment,
+  - [function](https://physcraper.readthedocs.io/en/latest/apidocs.html)
+    usage,
+  - finding and choosing a [starting
+    dataset](https://physcraper.readthedocs.io/en/latest/find-trees.html),
+  - [running](https://physcraper.readthedocs.io/en/latest/run.html) a
+    full analysis,
+  - [visualizing and
+    analysing](https://physcraper.readthedocs.io/en/latest/results.html)
+    results,
+  - real life
+    [examples](https://physcraper.readthedocs.io/en/latest/examples.html),
+    and
+  - tools for
+    [developers](https://physcraper.readthedocs.io/en/latest/CONTRIBUTING.html).
 
 :hamster: :palm\_tree: :frog: :ear\_of\_rice: :panda\_face: :tulip:
 :octopus: :blossom: :whale: :mushroom: :ant: :cactus: :fish:
 :maple\_leaf: :water\_buffalo: 🦠 :shell: :bug: :octocat:
 
-Physcraper relies on:
-
-  - [Dendropy](https://dendropy.org/primer/index.html): *Sukumaran, J
-    and MT Holder. 2010. DendroPy: a Python library for phylogenetic
-    computing. Bioinformatics 26: 1569-1571*
-    [doi.org/10.1093/bioinformatics/btq228](https://doi.org/10.1093/bioinformatics/btq228)
-    <br/><br/>
-  - [The Open Tree of Life
-    Project](https://tree.opentreeoflife.org/opentree/argus/opentree12.3@ott93302):
-    *Open Tree of Life, Benjamin Redelings, Luna Luisa Sanchez Reyes,
-    Karen A. Cranston, Jim Allman, Mark T. Holder, & Emily Jane
-    McTavish. (2019). Open Tree of Life Synthetic Tree (Version 12.3).
-    Zenodo*
-    [doi.org/10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)
-    <br/><br/>
-  - [OpenTree](https://github.com/OpenTreeOfLife/python-opentree):
-    *Emily Jane McTavish, Luna Luisa Sanchez Reyes, Mark T. Holder.
-    (2020). OpenTree: A Python package for Accessing and Analyzing data
-    from the Open Tree of Life. BioRxiv 2020.12.14.422759*
-    [doi.org/10.1101/2020.12.14.422759](https://doi.org/10.1101/2020.12.14.422759)
+## Citation
 
 If you use Physcraper, please cite:
 
-  - [Physcraper](https://www.biorxiv.org/content/10.1101/2020.09.15.299156v1.abstract):
-    *Luna Luisa Sanchez Reyes, Martha Kandziora, Emily Jane McTavish.
-    (2020). Physcraper: A Python package for continual update of
-    evolutionary estimates using the Open Tree of Life. BioRxiv
-    2020.09.15.299156*. doi:
-    [doi.org/10.1101/2020.09.15.299156](https://doi.org/10.1101/2020.09.15.299156)
+  - Sánchez-Reyes, L.L., M. Kandziora, & E.J McTavish. (2021).
+    *Physcraper: a Python package for continually updated phylogenetic
+    trees using the Open Tree of Life*. BMC Bioinformatics 22, 355. doi:
+    [doi.org/10.1186/s12859-021-04274-6](https://doi.org/10.1186/s12859-021-04274-6).
+    <br><br>
+  - Open Tree of Life, B. Redelings, L.L. Sanchez Reyes, K.A. Cranston,
+    J. Allman, M.T. Holder, & E.J. McTavish. (2019). *Open Tree of Life
+    Synthetic Tree (Version 12.3)*. Zenodo. doi:
+    [10.5281/zenodo.3937741](https://doi.org/10.5281/zenodo.3937741)
+
+## License
 
 Physcraper is made available through the [GNU General Public License
 v3.0](https://github.com/McTavishLab/physcraper/blob/main/LICENSE)
+
+## Contact
+
+The tool is under active development in the [McTavish
+Lab](https://mctavishlab.github.io/). Please post a GitHub issue
+[here](https://github.com/McTavishLab/physcraper/issues) or contact
+<ejmctavish@ucmerced.edu> if you need any help or have feedback.
+
+## Requirements
+
+Physcraper requires the user to install:
+
+  - [Anaconda](https://docs.anaconda.com/anaconda/install/) <br>
+    *Anaconda Software Distribution. Computer software. Vers. 4.8.0.
+    Anaconda, July. 2021. Web. <https://anaconda.com>*
+  - [Virtualenv](https://pypi.org/project/virtualenv/)
+  - [MUSCLE](https://www.ebi.ac.uk/Tools/msa/muscle/) <br> *Edgar RC.
+    MUSCLE: multiple sequence alignment with high accuracy and high
+    throughput. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7.* doi:
+    [10.1093/nar/gkh340](https://doi.org/10.1093/nar/gkh340)
+  - [RAxML](https://cme.h-its.org/exelixis/web/software/raxml/) <br>
+    *Stamatakis, Alexandros. “RAxML version 8: a tool for phylogenetic
+    analysis and post-analysis of large phylogenies.” Bioinformatics
+    30.9 (2014): 1312-1313.* doi:
+    [10.1093/bioinformatics/btu033](https://doi.org/10.1093/bioinformatics/btu033)
+  - [BLAST
+    +](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+    <br> This software is only needed if using a local genetic database.
+    Note that BLAST + is automatically installed when [installing
+    Physcraper using
+    Anaconda](https://physcraper.readthedocs.io/en/stable/install.html#anaconda-virtual-environment).
+    <br> *Camacho, C., Coulouris, G., Avagyan, V. et al. BLAST+:
+    architecture and applications. BMC Bioinformatics 10, 421 (2009).*
+    doi:
+    [10.1186/1471-2105-10-421](https://doi.org/10.1186/1471-2105-10-421)
+
+Physcraper relies on the following Python packages that are
+<b>automatically</b> installed:
+
+  - [argparse](https://docs.python.org/3/library/argparse.html)
+  - [biopython](https://biopython.org/) <br> *Cock, P. J., Antao, T.,
+    Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., et al. (2009).
+    Biopython: freely available Python tools for computational molecular
+    biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.*
+  - [configparser](https://docs.python.org/3/library/configparser.html)
+  - [coverage](https://coverage.readthedocs.io/)
+  - [DateTime](https://docs.python.org/3/library/datetime.html)
+  - [DendroPy](https://dendropy.org/primer/index.html) <br> *Sukumaran,
+    J and MT Holder. 2010. DendroPy: a Python library for phylogenetic
+    computing. Bioinformatics 26: 1569-1571* doi:
+    [10.1093/bioinformatics/btq228](https://doi.org/10.1093/bioinformatics/btq228)
+  - [future](https://python-future.org/)
+  - [m2r2](https://pypi.org/project/m2r2/)
+  - [nexson](https://github.com/OpenTreeOfLife/nexson)
+  - [numpy](https://numpy.org/) <br> *Harris, C. R., Millman, K. J., van
+    der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., …
+    Oliphant, T. E. (2020). Array programming with NumPy. Nature, 585,
+    357–362.* doi:
+    [10.1038/s41586-020-2649-2](https://doi.org/10.1038/s41586-020-2649-2)
+  - [OpenTree](https://github.com/OpenTreeOfLife/python-opentree) <br>
+    *Emily Jane McTavish, Luna Luisa Sanchez-Reyes, Mark T. Holder.
+    (2020). OpenTree: A Python package for Accessing and Analyzing data
+    from the Open Tree of Life. BioRxiv 2020.12.14.422759* doi:
+    [10.1101/2020.12.14.422759](https://doi.org/10.1101/2020.12.14.422759)
+  - [pandas](https://pandas.pydata.org/) <br> *McKinney, W., & others.
+    (2010). Data structures for statistical computing in python. In
+    Proceedings of the 9th Python in Science Conference (Vol. 445,
+    pp. 51–56).*
+  - [pytest](https://pytest.org/)
+  - [pytest-cov](https://pytest-cov.readthedocs.io/)
+  - [pytest-xdist](https://pypi.org/project/pytest-xdist/)
+  - [recommonmark](https://recommonmark.readthedocs.io/)
+  - [requests](https://docs.python-requests.org/) <br> *Chandra, R. V.,
+    & Varanasi, B. S. (2015). Python requests essentials. Packt
+    Publishing Ltd.*
+  - [sh](https://amoffat.github.io/sh/)
+  - [sphinx](https://www.sphinx-doc.org/)
+  - [urllib3](https://urllib3.readthedocs.io/)
diff --git a/bin/tree_comparison.py b/bin/tree_comparison.py
@@ -41,10 +41,10 @@
 
 
 parser = argparse.ArgumentParser()
-parser.add_argument("-d", "--results_dir", help="results directory from run")
+parser.add_argument("-d", "--dir", help="Physcraper output directory from a single run")
 parser.add_argument("-t1", "--original_tree", help="Original tree")
 parser.add_argument("-t2", "--updated_tree", help="Updated Tree")
-parser.add_argument("-otu", "--otu_info", help="File with taxon information JSON")
+parser.add_argument("-otu", "--otu_info", help="File with taxon information in JSON format")
 parser.add_argument("-og", "--outgroup", nargs='+', help="otu ids of outgroup taxa for rooting")
 parser.add_argument("-o", "--outputdir", help="Name for output directory")