Merge pull request #129 from kahsieh/master

New ROP

.gitignore

@@ -0,0 +1,111 @@
+# Project-specific
+db_*
+tools/imrep
+tools/metaphlan2
+tools/MiniConda
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+.static_storage/
+.media/
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

LICENSE.txt

@@ -1,31 +1,3 @@
-
-    Read Origin Protocol is a computational protocol for profiling the 
-    composition of unmapped reads, which failed to map to the human references. 
-    ROP profiles repeats, circRNAs, gene fusions, trans-splicing events, 
-    recombined B and T cell receptors and microbial communities.
-    Copyright (c) 2016 by Serghei Mangul ([email protected]), Harry Taegyun Yang 
-    ([email protected]), Kevin Hsieh ([email protected]), and Linus Chen 
-    ([email protected]). University of California, Los Angeles (UCLA). 
-
-    Read Origin Protocol is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    Read Origin Protocol is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-
-
-
-
-
-
                     GNU GENERAL PUBLIC LICENSE
                        Version 3, 29 June 2007
 

README.md

@@ -1,9 +1,100 @@
-# ROP: Read Origin Protocol
+# Read Origin Protocol
 
+The Read Origin Protocol (ROP) is a computational protocol that aims to
+discover the source of all reads, including those originating from complex RNA
+molecules, recombinant antibodies, and microbial communities. 
 
-The ROP protocol is available for free download as a package that is easy to install and run.  It provides a one-command solution to to discover the source of all unmapped reads, which originated from complex RNA molecules, recombinant B and T cell receptors and microbial communities. 
+Written by:
 
-ROP provides a flexible interface that allows users to perform analysis of interest, rather than running a full ROP analysis. For example,  `--microbiome` option allows to run only microbial analysis.   
+- Serghei Mangul (<[email protected]>)
+- Harry Taegyun Yang (<[email protected]>)
+- Kevin Hsieh (<[email protected]>)
+- Linus Chen (<[email protected]>)
 
-See the main webpage [https://github.com/smangul1/rop/wiki](https://github.com/smangul1/rop/wiki)
+at the University of California, Los Angeles (UCLA). 
 
+Released under the terms of the General Public License, version 3.0 (GPLv3).
+For more information, please visit: <https://github.com/smangul1/rop/wiki>
+
+## Installing ROP
+
+To install ROP, first clone this repository, then run
+
+```
+./install.sh
+```
+
+from the repository's directory. This will download dependencies and databases.
+The default installation will generally suffice, but the following options are
+available:
+
+- `-c|--clean`: Just remove installed tools.
+    - The installation script then must be re-run in order to use ROP again.
+- `-f|--force`: Unlink databases.
+    - Use with caution.
+- `-n|--native`: Use native python.
+    - MiniConda will not be downloaded.
+    - May lead to dependency errors.
+- `-l|--link LINK`: Link databases instead of downloading.
+    - Useful if you previously downloaded an ROP database.
+    - A symlink will be created in the current directory.
+- `-d|--db-dest DB_DEST` (default: `.`): Change database download location.
+    - Useful for managing space.
+    - A symlink will be created in the current directory.
+- `-o|--organism ORGANISM` (default: `human`): Organism to download databases
+  for.
+- `-s|--select-db SELECT_DB` (default: all): Database(s) to download for the
+  specified organism.
+    - A comma-separated list of one or more of the following: basic, repeats,
+      microbiome (which may be subdivided into metaphlan, viral, fungi,
+      protozoa).
+- `-h|--help`: Displays usage information.
+
+## Using ROP
+
+To use ROP, run
+
+```
+rop.sh unmapped_reads output_dir
+```
+
+Unless otherwise specified using an option, `unmapped_reads`
+must be a .fastq/.fq file, and `output_dir` must not exist (it will be created).
+Results will be written to `output_dir`, with one subdirectory for every stage
+of the pipeline. The following options are available:
+
+- `-o|--organism` (default: `human`): Run for the specified organism instead of
+  human.
+- `-s|--steps` (default: all except lowq and bacteria): Select the analysis
+  modes to use.
+    - A comma-separated list of one or more of the following: lowq, rdna,
+      reference, repeats, circrna, immune, microbiome (which may be subdivided
+      into bacteria, metaphlan, viral, fungi, protozoa).
+    - circrna and bacteria are not available in this release.
+    - `-s all` selects everything.
+- `-a|--fasta`: Input unmapped reads in .fasta format instead of .fastq format.
+  Forcibly disables low-quality read filtering.
+- `-b|--bam`: Input unmapped reads in .bam format instead of .fastq format.
+- `-z|--gzip`: gunzip the input file.
+- `-d|--dev`: Keep intermediate FASTA files.
+    - Consumes extra space.
+- `-f|--force`: Overwrite the analysis destination directory.
+- `-i|--ignore-extensions`: Ignore incorrect .fastq/.fq/.fasta/.fa file
+  extensions. Does not ignore incorrect .gz/.bam file extensions.
+- `-m|--max`: Use a liberal threshold when remapping to reference.
+    - May account for more reads.
+- `-x|--commands`: Print all commands (diagnostic mode).
+- `-h|--help`: Displays usage information.
+
+A small example file is included in the repository in various formats. To try it
+out, run one of the following commands from the repository directory:
+
+```
+rop.sh -b example/example.bam ropout
+rop.sh example/example.fastq ropout
+rop.sh -z example/example.fastq.gz ropout
+rop.sh -a example/example.fasta ropout
+rop.sh -az example/example.fasta.gz ropout
+```
+
+Then, browser to the `ropout` directory to see the analysis results!