added a manual

.gitignore

@@ -79,3 +79,6 @@ ehthumbs.db
 Thumbs.db
 
 *.gch
+
+.vscode/
+version.hpp
\ No newline at end of file

CHANGELOG

+
+Version 0.9.2-beta
+- added manual
+- changed RADIANT help message
+
 Version 0.9.1-beta
 - change of database construction and thereby much smaller databases
 - simpler handling of databases

docs/Makefile

+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = RADIANT
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/conf.py

+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'RADIANT'
+copyright = '2018, Carsten Kemena'
+author = 'Carsten Kemena'
+
+# The short X.Y version
+version = '0.9.2-beta'
+# The full version, including alpha/beta/rc tags
+release = '0.9.2-beta'
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+html_logo = '_static/logo.png'
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'RADIANTdoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    #'preamble': '',
+
+    'sphinxsetup':'VerbatimColor={rgb}{0.99,0.96,0.9},verbatimwithframe=false,warningBgColor={rgb}{1, 0.86,0.86},warningborder=2pt,warningBorderColor={rgb}{0.86, 0.08, 0.24},',
+    'classoptions': ',openany',
+
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+latex_additional_files = ["mystyle.sty"]
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'RADIANT.tex', 'RADIANT Manual',
+     'Carsten Kemena', 'manual'),
+]
+
+latex_logo = '_static/logo.png'
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'radiant', 'RADIANT Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'RADIANT', 'RADIANT Documentation',
+     author, 'RADIANT', 'One line description of project.',
+     'Miscellaneous'),
+]

docs/source/content/general.rst

+
+.. _general:
+
+************
+General
+************
+
+.. WARNING::
+    RADIANT is currently still in the beta-phase and therefore should be used with caution. However, our benchmark reveals that in most cases the results are very close to the (repeat collapsed) prediction of Pfam. But in a few cases RADIANT can miss quite a lot of domains.
+
+RADIANT is a program to annotate protein sequences with domains. 
+
+Website: https://domainworld.uni-muenster.de/programs/radiant/
+
+=========
+Algorithm
+=========
+
+RADIANT is based on the idea of UProC (P Meinicke, Bioinformatics 2015). It stores the words of known domains in a database and uses these words when scanning an unknown sequence to assign domains. Due to the algorithm it is currently not possible to detect domain repeats or provide start and end points of a domain.
+
+===============
+Contact
+===============
+
+If you have any problems, questions or suggestions concerning this program please contact us: domainWorld@uni-muenster.de
+

docs/source/content/installation.rst

+
+.. _installation:
+
+************
+Installation
+************
+
+------------
+Requirements
+------------
+
+We try to keep the dependencies as few as possible. Current dependencies are:
+
+ * BioSeqDataLib (https://ebbgit.uni-muenster.de/domainWorld/BioSeqDataLib) (can be added via git submodule)
+ * boost (http://www.boost.org)
+ * compiler with c++11
+
+--------
+Download
+--------
+
+You can currently choose between two different donwnload options: ``git`` and a manual download. Using ``git`` is the recommended way but if that is
+not possible you can use the manual way instead. Both ways are described in the next sections.
+
+Git
+^^^
+
+The easiest way to download the most current version of RADIANT is to use ``git``:
+
+.. code-block:: bash
+
+    git clone https://ebbgit.uni-muenster.de/domainWorld/RADIANT.git
+    cd RADIANT
+    git submodule init
+    git submodule update
+
+
+If you want to update to a newer version you can simply run the following command:
+
+.. code-block:: bash
+
+  git pull
+  git submodule update
+
+Do not forget to recombile the program after this step.
+
+Manual download
+^^^^^^^^^^^^^^^
+
+If you don't want to use git, you can download the source code from here: https://ebbgit.uni-muenster.de/domainWorld/RADIANT/-/archive/master/RADIANT-master.tar.gz.
+Below you find the commands needed to put everything necessary in its correct place. You can replace the ``wget`` command with manual downloads and copying the
+file to the correct position if you do not have an internet connection.
+
+.. code-block:: bash
+
+    wget https://ebbgit.uni-muenster.de/domainWorld/RADIANT/-/archive/master/RADIANT-master.tar.gz
+    tar xfz RADIANT-master.tar.gz
+
+    # The BioSeqDataLib now needs to be added manually
+    cd RADIANT-master/libs
+    rmdir BioSeqDataLib
+    wget https://ebbgit.uni-muenster.de/domainWorld/BioSeqDataLib/-/archive/master/BioSeqDataLib-master.tar.gz
+    tar xfz BioSeqDataLib-master.tar.gz
+    mv BioSeqDataLib-master BioSeqDataLib
+
+
+-----------
+Compilation
+-----------
+
+Change into the RADIANT directory and run the following commands:
+
+.. code-block:: bash
+
+    mkdir build
+    cd build
+    cmake ..
+    make
+
+

docs/source/content/radiant_usage.rst

+.. _rads:
+
+*************
+RADIANT Usage
+*************
+
+
+============
+Simple Usage
+============
+.. program:: radiant
+
+This section assumes that you have installed RADIANT as described in :ref:`installation` and setup RADIANT as described in :ref:`setup`.
+
+The minimal requirements are to provide an input sequence file (FASTA format) and the database folder. This prints the annotation to the console. Using the :option:`--out` option will write the annotation to a provided file. 
+
+
+.. code-block:: bash
+
+    # simplest RADIANT usage
+    radiant -i <input file> -d <database directory>
+
+    # write RADIANT output to file
+    radiant -i <input file> -d <database directory> -o <output file>
+
+===============
+Program Options
+===============
+
+
+---------------
+General options
+---------------
+
+The general option influence the general behaviour of RADS:
+
+.. program:: radiant
+
+.. option:: -h, --help
+
+    Prints a simple help message with a small description of all the available options.
+
+.. option:: -i <FILE>, --in <FILE>
+
+    The sequence file to annotate. If it is a DNA file, you have to use the :option:`--translate`  option to properly annotate the sequences. If you don't, protein domains will be predicted on the DNA which will not fail but give you wrong results.
+    
+.. option:: -d <DIRECTORY>, --database <DIRECTORY>
+
+    Prefix of the database. Can be either one of the precomputed ones downloaded from the website  (see :ref:`setup`)
+
+
+--------------
+Output options
+--------------
+
+The query options define the different ways a query can be provided.
+.. program:: radiant
+
+.. option:: -o <FILE>, --out <FILE>
+
+    The ouput file. If none is provided the annotation will be printed to the console.
+
+.. option:: -p, --pfam-like
+
+    Produces a Pfam-like output format. However, since not all colums can be filled with useful data, some of them will contain default values without meaning. This option is only meant to increase compatibility with existing parsers.
+
+.. option:: -n, --no-header
+
+    Prevents the output file header from being printed
+
+    
+
+-----------------
+Translate options
+-----------------
+
+These parameters influence the alignment scoring similar to the same values in a standard alignment.
+
+.. program:: radiant
+
+.. option:: --translate
+
+    Translate the input file from DNA into proteins. It will search for the longest ORF in all six frames and will translate that one into protein.
+
+
+    
+===============
+Output format
+===============
+
+The default output format contains a header with information about the used parameters. The actual annotation consists of 7 columns. The first columns denotes the name of the sequence. The second and third column contains the start and end of the domain, currently however that values are the same and can only be used to sort the domains to the correct order. The fourth column is the Pfam ID and the fifth contains the domain name. The last two columns contain the type and the clan of the annotated domain.
+
+
+Example output::
+
+    # RADIANT 0.9.2-beta
+    # RADIANT output format: 1.0
+    # run at Thu Nov 29 10:24:29 2018
+    #
+    # Options used:
+    #-----------------------------------------------------------------------------
+    # query file: example.fa
+    # database file: pfamdb_32_new/
+    # translate: false
+    #-----------------------------------------------------------------------------
+    #
+    # <seq id> <match start> <match end> <hmm acc> <hmm name> <type> <clan>
+
+    comp10000_c0_seq1|m.5390|g.5390        117    117 PF08209 Sgf11           Family      CL0361.4
+    comp10003_c0_seq1|m.5397|g.5397        379    379 PF10367 Vps39_2         Domain      No_clan
+    comp10010_c0_seq1|m.5409|g.5409        111    111 PF00117 GATase          Domain      CL0014.22
+    comp10011_c0_seq1|m.5412|g.5412         34     34 PF14632 SPT6_acidic     Family      No_clan
+    comp10011_c0_seq2|m.5414|g.5414         34     34 PF14632 SPT6_acidic     Family      No_clan
+    comp10012_c0_seq1|m.5416|g.5416        339    339 PF00096 zf-C2H2         Domain      CL0361.4
+    comp10015_c0_seq1|m.5426|g.5426         20     20 PF13358 DDE_3           Domain      CL0219.14
+    comp10017_c0_seq1|m.5429|g.5429         75     75 PF05915 DUF872          Family      No_clan
+    comp10019_c0_seq1|m.5433|g.5433        183    183 PF05182 Fip1            Motif       No_clan
+    comp10020_c0_seq1|m.5439|g.5439         27     27 PF00076 RRM_1           Domain      CL0221.11
+    comp10021_c0_seq1|m.5440|g.5440         41     41 PF00076 RRM_1           Domain      CL0221.11
+    comp10023_c0_seq1|m.5444|g.5444         70     70 PF14892 DUF4490         Family      No_clan
+    comp10023_c0_seq2|m.5446|g.5446         91     91 PF14892 DUF4490         Family      No_clan
+    comp10026_c0_seq1|m.5455|g.5455         98     98 PF12796 Ank_2           Repeat      CL0465.3
+    comp10027_c0_seq1|m.5459|g.5459         65     65 PF01490 Aa_trans        Family      CL0062.13
+    comp10028_c0_seq1|m.5463|g.5463         17     17 PF01398 JAB             Family      CL0366.4
+    comp10028_c0_seq1|m.5463|g.5463        108    108 PF13012 MitMem_reg      Family      No_clan
+    comp10029_c0_seq1|m.5466|g.5466         21     21 PF00578 AhpC-TSA        Domain      CL0172.17
+    comp10029_c0_seq1|m.5466|g.5466        176    176 PF10417 1-cysPrx_C      Domain      No_clan
+    comp10030_c0_seq1|m.5467|g.5467         47     47 PF14954 LIX1            Family      CL0196.12
+    comp10032_c0_seq1|m.5477|g.5477         82     82 PF00789 UBX             Domain      CL0072.20
+    comp10032_c0_seq2|m.5478|g.5478         18     18 PF00627 UBA             Domain      CL0214.13
+    comp10032_c0_seq2|m.5478|g.5478        293    293 PF00789 UBX             Domain      CL0072.20
+    comp10034_c0_seq1|m.5482|g.5482         86     86 PF00595 PDZ             Domain      CL0466.3
+    comp10036_c0_seq1|m.5489|g.5489         18     18 PF05021 NPL4            Family      CL0366.4
+    comp10036_c0_seq2|m.5492|g.5492         58     58 PF05021 NPL4            Family      CL0366.4
+    comp10037_c0_seq1|m.5494|g.5494         53     53 PF12436 USP7_ICP0_bdg   Family      CL0072.20
+    comp10037_c0_seq1|m.5494|g.5494        283    283 PF14533 USP7_C2         Family      CL0072.20
+    comp10037_c0_seq2|m.5504|g.5504         53     53 PF12436 USP7_ICP0_bdg   Family      CL0072.20
+    comp10037_c0_seq2|m.5504|g.5504        283    283 PF14533 USP7_C2         Family      CL0072.20

docs/source/content/setup.rst

+
+.. _setup:
+
+******************
+Setting up RADIANT
+******************
+
+This chapter describes how to setup RADIANT so it can access all the data it needs.
+
+
+=======================
+Setting up the database
+=======================
+
+You can download the database from the `DomainWorld website <https://domainworld.uni-muenster.de/programs/radiant/#radiant-data-bases>`_. Simply download the database for the Pfam version you want to use and then extract the file using tar:
+
+.. code-block:: bash
+    
+    # replace <version> with the version you downloaded
+    tar xfj radiant_db_pfam<version>.tar.bz2
+    
+The command will create a new directory containing three files needed by RADIANT. You will simply need to provide the path to the folder to RADIANT.

docs/source/index.rst

+.. RADIANT documentation master file, created by
+   sphinx-quickstart on Wed Nov 28 16:21:21 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to RADIANT's documentation!
+===================================
+
+.. toctree::
+    :maxdepth: 2
+    :caption: Contents:
+
+    content/general.rst
+    content/installation.rst
+    content/setup.rst
+    content/radiant_usage.rst
+
+.. only:: html
+    
+    Indices and tables
+    ==================
+
+    * :ref:`genindex`
+    * :ref:`search`

src/makeRadiantDb.cpp

@@ -8,13 +8,13 @@ namespace fs = boost::filesystem;
 /**
  * \brief Write database to file
  * @param database The database to write
- * @param  outFile The file to write the database into
+ * @param  outDir The file to write the database into
  */
 void
-write2file(std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short > > &database, const std::string &outFile)
+write2file(std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short > > &database, const std::string &outDir)
 {
 
-	std::ofstream fout(outFile, std::ios::out | std::ios::binary);
+	std::ofstream fout(outDir, std::ios::out | std::ios::binary);
 	size_t val= database.size();
 	fout.write((char*)&val, sizeof(size_t));
 	for (auto it=database.begin(); it!=database.end(); ++it)
@@ -31,8 +31,8 @@ write2file(std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short >
  	fout.close();
 	
 /*
-	std::ofstream fout(outFile, std::ios::out | std::ios::binary);
-	std::ofstream fout_index(outFile+".index", std::ios::out | std::ios::binary);
+	std::ofstream fout(outDir, std::ios::out | std::ios::binary);
+	std::ofstream fout_index(outDir+".index", std::ios::out | std::ios::binary);
 	size_t val= database.size();
 	fout.write((char*)&val, sizeof(size_t));
 	for (auto it=database.begin(); it!=database.end(); ++it)
@@ -59,15 +59,15 @@ write2file(std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short >
 int
 main(int argc, char const *argv[])
 {
-	fs::path inFile, outFile;
+	fs::path inFile, outDir;
 	size_t nThreads;
 	std::string radiantDBVersion(std::string(STR(MAJOR_VERSION)) + "." + std::string(STR(MINOR_VERSION)) + "." + std::string(STR(PATCH_VERSION)) );
 	po::options_description allOpts("makeRadiantDB " + radiantDBVersion + " (C) 2017  Carsten Kemena\nThis program comes with ABSOLUTELY NO WARRANTY;\n\nAllowed options are displayed below.");
 	po::options_description general("General options");
 	general.add_options()
 		("help,h", "Produces this help message")
-		("in,i", po::value<fs::path>(&inFile)->required(), "The input file")
-		("out,o", po::value<fs::path>(&outFile)->required(), "The prefix for the output files")
+		("in,i", po::value<fs::path>(&inFile)->required()->value_name("FILE"), "The input file")
+		("out,o", po::value<fs::path>(&outDir)->required()->value_name("DIRECTORY"), "The prefix for the output files")
 		("nThreads,t", po::value<size_t>(&nThreads)->default_value(1), "The number of threads to use")
 	;
 
@@ -95,12 +95,12 @@ main(int argc, char const *argv[])
 	omp_set_num_threads(nThreads);
 	std::unordered_map<PrefixType, std::map<CodedSuffix, unsigned short > > database;
 	turnFile2db(inFile, database, false);
-	write2file(database, outFile.string() + "_fwd.db");
+	write2file(database, outDir.string() + "/forward.db");
 
 	database.clear();
 	turnFile2db(inFile, database, true);
 	cout << "Write to file" << endl;
-	write2file(database, outFile.string() + "_rev.db");
+	write2file(database, outDir.string() + "/reverse.db");
 
 	return 0;
 }

src/radiant.cpp

@@ -265,8 +265,8 @@ main(int argc, char const *argv[])
 		po::options_description general("General options");
 		general.add_options()
 			("help,h", "Produces this help message")
-			("in,i", po::value<fs::path>(&inFile)->required(), "The input file")
-			("database,d", po::value<fs::path>(&databaseFile)->required(), "The path to the database")
+			("in,i", po::value<fs::path>(&inFile)->required()->value_name("FILE"), "The input file")
+			("database,d", po::value<fs::path>(&databaseFile)->required()->value_name("DIRECTORY"), "The path to the database")
 			//("nThreads,t", po::value<int>(&nThreads)->default_value(1), "Number of threads to use")
 		;
 
@@ -274,7 +274,7 @@ main(int argc, char const *argv[])
 		bool pfamLike, noHeader;
 		po::options_description outputO("Output options");
 		outputO.add_options()
-			("out,o", po::value<fs::path>(&outFile), "The output file")
+			("out,o", po::value<fs::path>(&outFile)->value_name("FILE"), "The output file")
 			("pfam-like,p", po::value<bool>(&pfamLike)->default_value(false)->zero_tokens(), "Produces a fake Pfam format")
 			("no-header,n", po::value<bool>(&noHeader)->default_value(false)->zero_tokens(), "Do not print the header")
 		;

tests/CMakeLists.txt

 
-SET(unit_tests_src ./unit_tests.cpp)
-SET(unit_tests_exe unit_tests)
-ADD_EXECUTABLE(${unit_tests_exe} ${unit_tests_src})
-target_link_libraries(${unit_tests_exe}
+
+
+#SET(unit_tests_src ./unit_tests.cpp)
+#SET(unit_tests_exe unit_tests)
+#ADD_EXECUTABLE(${unit_tests_exe} ${unit_tests_src})
+#target_link_libraries(${unit_tests_exe}
+#	${Boost_LIBRARIES}
+#)
+
+
+FUNCTION(PREPEND var prefix)
+   SET(listVar "")
+   FOREACH(f ${ARGN})
+      LIST(APPEND listVar "${prefix}${f}")
+   ENDFOREACH(f)
+   SET(${var} "${listVar}" PARENT_SCOPE)
+ENDFUNCTION(PREPEND)
+
+SET(tests_src ./unitTests/unit_tests.cpp)
+SET(tests_exe unit_tests)
+ADD_EXECUTABLE(${tests_exe} ${tests_src})
+target_link_libraries(${tests_exe}
 	${Boost_LIBRARIES}
 )

tests/integrationTests/run_tests.sh

+#!/usr/bin/env bats
+
+@test "simple_run"
+{
+    
+}
+
+@test "make DB Test" {
+	# database based on pfam annotation files
+	run ../../build/makeRadsDB -i ../data/db_pfam.dom -s ../data/db_seqs.fa -o annotation
+	[ $status == 0 ]
+	echo $output
+	[ "$output" == $'Number of sequences included: 8\nNumber of distinct arrangements 7' ]
+	rm annotation.db annotation.da
+
+	# database based on interpro file
+	run ../../build/makeRadsDB -I ../data/match_small.xml -o interPro -d PFAM
+	[ $status == 0 ]
+	[ "$output" == $'Number of sequences included: 10\nNumber of distinct arrangements 9' ]
+}
+
+@test "run RADS Test" {
+
+	run ../../build/rads -d interPro -Q ../data/query_seqs.fa -o testQuerySeq.txt -m pfam-31.dsm
+	[ $status == 0 ]
+	run diff <(grep -v '#' testQuerySeq.txt) <(grep -v '#' results/testQuerySeqRes.txt)
+	[ $status == 0 ]
+
+	# check if all parameter works
+	#run ../../build/rads -D PF00733 PF13537 -a -m pfam-31.dsm -d interPro
+	#[ $status == 0 ]
+	#[ "$output" == $'# RADS version 2.1.0\n# RADS Output v1\n# ********************************\n\n# -------------------------------------------------------------------\nResults for: manual entered query\nDomain arrangement: PF00733 PF13537\n\n# score | normalized | SeqID | sequence length | domain arrangement\n# -------------------------------------------------------------------\n200	1.00	A0A004	645	PF00733 240 626 PF13537 49 162' ]
+
+	run ../../build/rads -D PF00733 PF13537 -m pfam-31.dsm -d interPro -o test1Res.txt
+	[ $status == 0 ]
+	run diff <(grep -v '#' test1Res.txt) <(grep -v '#' results/test1Res.txt)
+	[ $status == 0 ]
+
+	run ../../build/rads -h
+	[ $status == 0 ]
+
+	rm test1Res.txt testQuerySeq.txt
+	rm interPro.db interPro.da
+}

tests/encode_Test.hpp → tests/unitTests/encode_Test.hpp

@@ -7,8 +7,8 @@
 #include <iostream>
 #include <string>
 
-#include "../src/common.hpp"
-#include "../libs/BioSeqDataLib/src/sequence/Sequence.hpp"
+#include "../../src/common.hpp"
+#include "../../libs/BioSeqDataLib/src/sequence/Sequence.hpp"
 
 BOOST_AUTO_TEST_SUITE(Encode_Test)
 

tests/makeDB_Test.hpp → tests/unitTests/makeDB_Test.hpp

@@ -7,9 +7,9 @@
 #include <iostream>
 #include <string>
 
-#include "../src/common.hpp"
-#include "../src/makeRadiantDb.hpp"
-#include "../libs/BioSeqDataLib/src/sequence/SequenceSet.hpp"
+#include "../../src/common.hpp"
+#include "../../src/makeRadiantDb.hpp"
+#include "../../libs/BioSeqDataLib/src/sequence/SequenceSet.hpp"
 
 BOOST_AUTO_TEST_SUITE(MakeDB_Test)