From eb37c2b59db37e459478fcc069b0cf7cecdb674a Mon Sep 17 00:00:00 2001 From: Alexey Gurevich Date: Fri, 29 Mar 2019 18:18:22 +0300 Subject: [PATCH] NPDtools 2.4.0 release: docs update --- CHANGES.txt | 5 +++++ README.md | 45 +++++++++++++++++++++++++++++---------------- VERSION.txt | 2 +- 3 files changed, 35 insertions(+), 17 deletions(-) diff --git a/CHANGES.txt b/CHANGES.txt index 7a8e002..c6934a5 100644 --- a/CHANGES.txt +++ b/CHANGES.txt @@ -1,4 +1,9 @@ +## 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. diff --git a/README.md b/README.md index 082997e..f644eeb 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -__NPDtools 2.3.0 Manual__ +__NPDtools 2.4.0 Manual__ * [About NPDtools](#sec_intro) * [Package content](#sec_intro_content) @@ -28,7 +28,7 @@ This manual will help you to install and run NPDtools. The latest version of the manual is available online at . All projects news are at . -NPDtools version 2.3.0 was released under the Apache 2.0 License on January 9, 2019 +NPDtools version 2.4.0 was released under the Apache 2.0 License on March 29, 2019 and can be downloaded from . The software is developed in collaboration of [Saint Petersburg State University](http://cab.spbu.ru) (Russia), [University of California San Diego](http://cseweb.ucsd.edu/~ppevzner/) (CA, USA) @@ -70,7 +70,9 @@ NPDtools requires a 64-bit Linux system or macOS and Python 2.7 to be pre-instal The MetaMiner pipeline also requires [GNU sed](https://www.gnu.org/software/sed/) to be present in the `PATH` environment variable as `sed` (this is always true for Linux systems but may require additional configurations on macOS since -GNU sed is usually installed there as `gsed`). +GNU sed is usually installed there as `gsed`). For presenting Spectral Network propagation graphs, +MetaMiner also requires `matplotlib` and `networkx` Python libraries. If they are not installed, +the propagation will be generated in a plain text format only (see `--spec-network` option). You can also use NPDtools pipelines online on the [GNPS platform](https://gnps.ucsd.edu/ProteoSAFe/static/gnps-theoretical.jsp). In this case, a registration is needed but it is quick and simple. @@ -92,13 +94,13 @@ In case of successful installation the following files should be present in the ## Downloading NPDtools binaries for Linux -To download [NPDtools Linux binaries](https://github.com/ablab/npdtools/releases/download/npdtools-2.3.0/NPDtools-2.3.0-Linux.tar.gz) +To download [NPDtools Linux binaries](https://github.com/ablab/npdtools/releases/download/npdtools-2.4.0/NPDtools-2.4.0-Linux.tar.gz) and extract them, go to the directory in which you wish NPDtools to be installed and run: ``` bash - wget https://github.com/ablab/npdtools/releases/download/npdtools-2.3.0/NPDtools-2.3.0-Linux.tar.gz - tar -xzf NPDtools-2.3.0-Linux.tar.gz - cd NPDtools-2.3.0-Linux + wget https://github.com/ablab/npdtools/releases/download/npdtools-2.4.0/NPDtools-2.4.0-Linux.tar.gz + tar -xzf NPDtools-2.4.0-Linux.tar.gz + cd NPDtools-2.4.0-Linux ``` We further refer to this directory as ``. @@ -109,13 +111,13 @@ so consider adding this subdirectory to the `PATH` variable. ## Downloading NPDtools binaries for macOS -To download [NPDtools macOS binaries](https://github.com/ablab/npdtools/releases/download/npdtools-2.3.0/NPDtools-2.3.0-Darwin.tar.gz) +To download [NPDtools macOS binaries](https://github.com/ablab/npdtools/releases/download/npdtools-2.4.0/NPDtools-2.4.0-Darwin.tar.gz) and extract them, go to the directory in which you wish NPDtools to be installed and run: ``` bash - curl -L https://github.com/ablab/npdtools/releases/download/npdtools-2.3.0/NPDtools-2.3.0-Darwin.tar.gz -o NPDtools-2.3.0-Darwin.tar.gz - tar -xzf NPDtools-2.3.0-Darwin.tar.gz - cd NPDtools-2.3.0-Darwin + curl -L https://github.com/ablab/npdtools/releases/download/npdtools-2.4.0/NPDtools-2.4.0-Darwin.tar.gz -o NPDtools-2.4.0-Darwin.tar.gz + tar -xzf NPDtools-2.4.0-Darwin.tar.gz + cd NPDtools-2.4.0-Darwin ``` We further refer to this directory as ``. @@ -506,17 +508,28 @@ or [antiSMASH](https://antismash.secondarymetabolites.org)'s `.final.gbk`). MetaMiner specific options are: `-a` (or `--antismash`) Sequence files are antiSMASH output (`.final.gbk`). If not specified, the input files are expected to - be raw genome nucleotide sequences in FASTA format (see also `--boa` option). Tested with antiSMASH v.2 output. + be raw genome nucleotide sequences in FASTA format (see also `--ripp` option). Tested with antiSMASH v.2 output. -`--boa` - Sequence files are BOA output (protein `.fasta`). If not specified, the input files are expected to +`--ripp` + Sequence files are already predicted and translated RiPP sequences (protein `.fasta`), e.g. it is BOA output. + If not specified, the input files are expected to be raw genome nucleotide sequences in FASTA format (see also `--antismash` option). `-c ` (or `--class `) Class of RiPPs to look for. Valid choices are: 'formylated', 'glycocin', 'lantibiotic', 'lap', 'lassopeptide', 'linaridin', 'proteusin', 'cyanobactin', and 'methanobactin'. You can also specify 'all' to try all classes one by one. - *The default value is 'lantibiotic'*. + *The default value is 'lantibiotic'*. + +`--blind` + Enable search in a blind mode, i.e. search for new PTMs with arbitrary mass shifts. Could be very slow. + +`--spec-network` + Path to the Spectral Network output + ([GNPS Data Analysis workflow](https://gnps.ucsd.edu/ProteoSAFe/index.jsp?params=%7B%22workflow%22:%22METABOLOMICS-SNETS-V2%22,%22library_on_server%22:%22d.speclibs;%22%7D) + also known as Molecular Networking). If specified, MetaMiner will identify connected components related + to the most significant RiPP identifications and report them in plain text and graphical formats + (saved under `/spec_nets/`). #### Usage example A sample run of MetaMiner may look like this: @@ -533,7 +546,7 @@ See important notes on specifying paths of the running script and `test_data` in [beginning of this section](#sec_running). If the run is finished correctly, you will see identification of a lantibiotic with "TGSQVSLLVCEYSSLSVVLCTP" original sequence -and "T-18GS-18QVS-18LLVCEYS-18SLSVVLCTP" sequence after modifications in `dereplicator_outdir/significant_matches.tsv`. +and "T-18GS-18QVS-18LLVCEYS-18SLSVVLCTP" sequence after modifications in `metaminer_outdir/significant_matches.tsv`. The modifications "T-18" and "S-18" correspond to dehydrobutyrine and dehydroalanine, respectively. These sequences correspond to AmfS peptide, you may read more about it in [Ueda et al, 2002](https://www.ncbi.nlm.nih.gov/pubmed/11844785). diff --git a/VERSION.txt b/VERSION.txt index 276cbf9..197c4d5 100644 --- a/VERSION.txt +++ b/VERSION.txt @@ -1 +1 @@ -2.3.0 +2.4.0