NPDtools 2.5.0 release: docs update

ablab · Nov 28, 2019 · 889ff01 · 889ff01
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diff --git a/CHANGES.txt b/CHANGES.txt
diff --git a/README.md b/README.md
diff --git a/VERSION.txt b/VERSION.txt
diff --git a/docs/CHANGES.txt b/docs/CHANGES.txt
@@ -0,0 +1,29 @@
+
+## NPDtools 2.5.0, 28 November 2019
+* NEW: Added NPS method in Dereplicator/VarQuest (see --nps)
+* NEW: Added support for Python3
+* NEW: Added --debug, --reuse, and --version options
+* CHANGE: Improved documentation and test data for MetaMiner
+* CHANGE: Auto-detection of sequence file type in MetaMiner
+* FIX: Fixed parsing of MGF files with uncommon fields (once more)
+
+## NPDtools 2.4.0, 29 March 2019
+* NEW: Added SpecNets propagation in MetaMiner (see --spec-network)
+* NEW: Added blind search mode in MetaMiner (see --blind)
+* CHANGE: Improvements in performance of Dereplicator+
+
+## NPDtools 2.3.0, 9 January 2019
+* NEW: Added manual
+* CHANGE: MetaRiPPquest renamed to MetaMiner
+* CHANGE: Improvements in performance and functionality of MetaMiner
+
+## NPDtools 2.2.0, 21 June 2018
+* NEW: Added Dereplicator+
+* FIX: Fixed parsing of MGF files with uncommon fields
+
+## NPDtools 2.1.0, 9 February 2018
+* NEW: Added MetaRiPPquest
+* FIX: Multiple bugfixes (mostly in Dereplicator)
+
+## NPDtools 2.0.0, 21 September 2017
+* Initial public release. Includes Dereplicator and VarQuest
diff --git a/LICENSE.txt → docs/LICENSE.txt b/LICENSE.txt → docs/LICENSE.txt
@@ -50,6 +50,13 @@ Amina Bouslimani, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A
 Luke R Thompson, Md-Nafiz Hamid, James T Morton, Alla Mikheenko, Alexander Shlemov,
 Anton Korobeynikov, Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick,
 Lena Gerwick, Peter C. Dorrestein, Pavel A. Pevzner, Hosein Mohimani.
-MetaMiner: A Peptidogenomics Approach for the Discovery of Ribosomally
-Synthesized and Post-translationally Modified Peptides.
-Submitted, 2019
+MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal
+Peptide Natural Products with Blind Modifications from Microbial Communities
+Cell Systems, 2019. doi: 10.1016/j.cels.2019.09.004
+First published online: October 16, 2019
+
+Azat M Tagirdzhanov, Alexander Shlemov, Alexey Gurevich.
+NPS: scoring and evaluating the statistical significance of peptidic natural
+product–spectrum matches.
+Bioinformatics, 2019. doi: 10.1093/bioinformatics/btz374
+First published online: July 5, 2019
diff --git a/docs/MetaMiner.md b/docs/MetaMiner.md
diff --git a/docs/MetaMiner_fig.png b/docs/MetaMiner_fig.png
diff --git a/docs/README_short.txt b/docs/README_short.txt
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+NPDtools
+Natural Product Discovery tools
+Version: see VERSION.txt
+License: see LICENSE.txt
+
+Developed in Saint Petersburg State University, St. Petersburg, Russia
+Developed in University of California San Diego, La Jolla, CA, USA
+Developed in Carnegie Mellon University, Pittsburgh, PA, USA
+
+The package contains:
+* DEREPLICATOR: in silico identification of peptidic natural products through database search of mass spectra
+* VarQuest: modification-tolerant identification of novel variants of peptidic antibiotics and other natural products
+* MetaMiner: a peptidogenomics approach for the discovery of ribosomally synthesized and post-translationally modified peptides
+* Dereplicator+: indentification of metabolites through database search of mass spectra
+* NPS: scoring and evaluating the statistical significance of peptidic natural product–spectrum matches (a part of Dereplicator and VarQuest)
+
+
+Usage examples:
+    ./bin/dereplicator.py \
+            --db-path share/npdtools/test_data/sample_database/ \
+            -o dereplicator_test_output_dir \
+            share/npdtools/test_data/dereplicator/
+
+    ./bin/varquest.py \
+            --db-path share/npdtools/test_data/sample_database/ \
+            -o varquest_test_output_dir \
+            share/npdtools/test_data/varquest/
+
+    ./bin/metaminer.py \
+            -o metaminer_test_output_dir \
+            share/npdtools/test_data/metaminer/ \
+            -s share/npdtools/test_data/metaminer/
+
+    ./bin/dereplicator+.py \
+            --db-path share/npdtools/test_data/sample_database/ \
+            -o dereplicator+_test_output_dir \
+            share/npdtools/test_data/dereplicator+/
+
+For the full list of available options please run
+    ./bin/dereplicator.py --help
+    ./bin/varquest.py --help
+    ./bin/metaminer.py --help
+    ./bin/dereplicator+.py --help
+
+
+Output:
+    significant_matches.tsv          list of the most reliable metabolite-spectrum matches
+    significant_unique_matches.tsv   list of the most reliable unique metabolite identifications
+    summary.tsv                      short summary report
+
+
+System requirements:
+- Linux or macOS
+- Python 2.6-2.7 or Python 3.3+
+
+
+Contacts and additional information:
+    [email protected]
+    http://cab.spbu.ru/software/dereplicator
+    http://cab.spbu.ru/software/varquest
+    http://cab.spbu.ru/software/metaminer
+    http://cab.spbu.ru/software/dereplicator-plus
+    http://cab.spbu.ru/software/nps
+
+
+References: see LICENSE.txt
diff --git a/docs/VERSION.txt b/docs/VERSION.txt
@@ -0,0 +1 @@
+2.5.0
diff --git a/test_data/.DS_Store b/test_data/.DS_Store
diff --git a/test_data/dereplicator+/chalcomycin.mgf b/test_data/dereplicator+/chalcomycin.mgf
diff --git a/test_data/dereplicator+/surugamide.mgf b/test_data/dereplicator+/surugamide.mgf