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For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights. +Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements. +Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material. +License Elements means the license attributes listed in the name of a Creative Commons Public License. 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The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material. +Downstream recipients. +Offer from the Licensor – Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License. +Additional offer from the Licensor – Adapted Material. Every recipient of Adapted Material from You automatically receives an offer from the Licensor to exercise the Licensed Rights in the Adapted Material under the conditions of the Adapter’s License You apply. +No downstream restrictions. 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Nothing in this Public License constitutes or may be construed as permission to assert or imply that You are, or that Your use of the Licensed Material is, connected with, or sponsored, endorsed, or granted official status by, the Licensor or others designated to receive attribution as provided in Section 3(a)(1)(A)(i). +Other rights. + +Moral rights, such as the right of integrity, are not licensed under this Public License, nor are publicity, privacy, and/or other similar personality rights; however, to the extent possible, the Licensor waives and/or agrees not to assert any such rights held by the Licensor to the limited extent necessary to allow You to exercise the Licensed Rights, but not otherwise. +Patent and trademark rights are not licensed under this Public License. +To the extent possible, the Licensor waives any right to collect royalties from You for the exercise of the Licensed Rights, whether directly or through a collecting society under any voluntary or waivable statutory or compulsory licensing scheme. In all other cases the Licensor expressly reserves any right to collect such royalties, including when the Licensed Material is used other than for NonCommercial purposes. +Section 3 – License Conditions. + +Your exercise of the Licensed Rights is expressly made subject to the following conditions. + +Attribution. + +If You Share the Licensed Material (including in modified form), You must: + +retain the following if it is supplied by the Licensor with the Licensed Material: +identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated); +a copyright notice; +a notice that refers to this Public License; +a notice that refers to the disclaimer of warranties; +a URI or hyperlink to the Licensed Material to the extent reasonably practicable; +indicate if You modified the Licensed Material and retain an indication of any previous modifications; and +indicate the Licensed Material is licensed under this Public License, and include the text of, or the URI or hyperlink to, this Public License. +You may satisfy the conditions in Section 3(a)(1) in any reasonable manner based on the medium, means, and context in which You Share the Licensed Material. For example, it may be reasonable to satisfy the conditions by providing a URI or hyperlink to a resource that includes the required information. +If requested by the Licensor, You must remove any of the information required by Section 3(a)(1)(A) to the extent reasonably practicable. +ShareAlike. +In addition to the conditions in Section 3(a), if You Share Adapted Material You produce, the following conditions also apply. + +The Adapter’s License You apply must be a Creative Commons license with the same License Elements, this version or later, or a BY-NC-SA Compatible License. +You must include the text of, or the URI or hyperlink to, the Adapter's License You apply. You may satisfy this condition in any reasonable manner based on the medium, means, and context in which You Share Adapted Material. +You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, Adapted Material that restrict exercise of the rights granted under the Adapter's License You apply. +Section 4 – Sui Generis Database Rights. + +Where the Licensed Rights include Sui Generis Database Rights that apply to Your use of the Licensed Material: + +for the avoidance of doubt, Section 2(a)(1) grants You the right to extract, reuse, reproduce, and Share all or a substantial portion of the contents of the database for NonCommercial purposes only; +if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material, including for purposes of Section 3(b); and +You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database. +For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights. +Section 5 – Disclaimer of Warranties and Limitation of Liability. + +Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You. +To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You. +The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability. +Section 6 – Term and Termination. + +This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically. +Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates: + +automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or +upon express reinstatement by the Licensor. +For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License. +For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License. +Sections 1, 5, 6, 7, and 8 survive termination of this Public License. +Section 7 – Other Terms and Conditions. + +The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed. +Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License. +Section 8 – Interpretation. + +For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License. +To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions. +No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor. +Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority. diff --git a/README.md b/README.md index 8d00c35..2105bdc 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ # stringMLST + Fast k-mer based tool for multi locus sequence typing (MLST) stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform-independent fashion with minimum dependencies. @@ -17,6 +18,10 @@ keeping your databases updated, stringMLST can download and build databases from and profile definitions. Please see the "Included databases and automated retrieval of databases from pubMLST" section below for instructions. *The databases bundled here are for convenience only, do not rely on them being up-to-date*. +stringMLST is licensed and distributed under [CC Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)](https://creativecommons.org/licenses/by-nc-sa/4.0) +and is free for academic users and requires permission before any commercial use for any version of this code/algorithm. +If you are a commercial user, please contact king.jordan@biology.gatech.edu for permissions + ## Recommended installation method ``` @@ -28,7 +33,8 @@ pip install stringMLST ``` git clone https://github.com/jordanlab/stringMLST -# Optional, download prebuilt databases +# Optional, download prebuilt databases +# We don't recommend this method, instead build the databases locally cd stringMLST git submodule init git submodule update diff --git a/README.rst b/README.rst index 02dd451..a972751 100644 --- a/README.rst +++ b/README.rst @@ -7,20 +7,64 @@ sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform-independent fashion with minimum dependencies. -Reference *http://jordan.biology.gatech.edu/page/software/stringmlst/* +| Reference +| *http://jordan.biology.gatech.edu/page/software/stringmlst/* + +| Abstract +| *http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.short?rss=1* + +| Application Note +| *http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.full.pdf+html* + +**stringMLST is a *tool* not a *database*, always use the most +up-to-date database files as possible.** To facilitate keeping your +databases updated, stringMLST can download and build databases from +pubMLST using the most recent allele and profile definitions. Please see +the "Included databases and automated retrieval of databases from +pubMLST" section below for instructions. *The databases bundled here are +for convenience only, do not rely on them being up-to-date*. + +| stringMLST is licensed and distributed under `CC + Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA + 4.0) `__ +| and is free for academic users and requires permission before any + commercial use for any version of this code/algorithm. +| If you are a commercial user, please contact + king.jordan@biology.gatech.edu for permissions + +Recommended installation method +------------------------------- -Abstract -*http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.short?rss=1* +:: -Application Note -*http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.full.pdf+html* + pip install stringMLST -Installing stringMLST via pip ------------------------------ +Installation via git (Not recommended for most users) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ :: - pip install stringMLST + git clone https://github.com/jordanlab/stringMLST + # Optional, download prebuilt databases + # We don't recommend this method, instead build the databases locally + cd stringMLST + git submodule init + git submodule update + +Quickstart guide +---------------- + +.. code:: bash + + pip install stringMLST + mkdir -p stringMLST_analysis; cd stringMLST_analysis + stringMLST.py --getMLST -P neisseria/nmb --species neisseria + # Download all available databases with: + # stringMLST.py --getMLST -P mlst_dbs --species all + wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_1.fastq.gz ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR026/ERR026529/ERR026529_2.fastq.gz + stringMLST.py --predict -P neisseria/nmb -1 ERR026529_1.fastq.gz -2 ERR026529_2.fastq.gz + Sample abcZ adk aroE fumC gdh pdhC pgm ST + ERR026529 231 180 306 612 269 277 260 10174 Python dependencies and external programs ----------------------------------------- @@ -44,7 +88,7 @@ stringMLST has been tested with: To install the dependencies ~~~~~~~~~~~~~~~~~~~~~~~~~~~ -:: +.. code:: bash # pyfaidx pip install --user pyfaidx @@ -81,7 +125,9 @@ Usage for Example Read Files (Neisseria meningitidis) - Extract the MLST loci dataset. -``unzip datasets/Neisseria_spp.zip -d datasets`` +:: + + unzip datasets/Neisseria_spp.zip -d datasets - Create or use a config file specifying the location of all the locus and profile files. Example config file (Neisseria\_spp/config.txt): @@ -255,10 +301,10 @@ FASTQ files provided in a list file Optional arguments -1,--fastq1 = Path to first fastq file for paired end sample and path to the fastq file for single end file. - Should have extention fastq or fq. + Should have extension fastq or fq. -2,--fastq2 = Path to second fastq file for paired end sample. - Should have extention fastq or fq. + Should have extension fastq or fq. -d,--dir,--directory = BATCH MODE : Location of all the samples for batch mode. -C,--coverage @@ -342,10 +388,10 @@ NA10831\_ATCACG\_L002\_R1\_001.fastq.gz ## Running stringMLST - #### Inlcuded databases and automated retrieval of databases from pubMLST + #### Included databases and automated retrieval of databases from pubMLST stringMLST includes all the pubMLST databases as of **February 15, 2017**, built with the default kmer (*35*). They can be found in the `datasets/` folder. - Simply unzip the databases you need and begin using stringMSLT as desbribed below. + Simply unzip the databases you need and begin using stringMSLT as described below. All the databases from pubMLST can be downloaded and prepared with your kmer choice @@ -357,7 +403,7 @@ stringMLST.py --getMLST -P datasets/ --species all - Individual databases from pubMLST can also be downloaded as needed, using the scheme indentifiers + Individual databases from pubMLST can also be downloaded as needed, using the scheme identifiers *Downloading a scheme* diff --git a/setup.cfg b/setup.cfg index b88034e..5aef279 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,2 +1,2 @@ [metadata] -description-file = README.md +description-file = README.rst diff --git a/setup.py b/setup.py index 3449c62..9175eac 100644 --- a/setup.py +++ b/setup.py @@ -5,11 +5,17 @@ except ImportError: from distutils.core import setup +here = path.abspath(path.dirname(__file__)) +long_description="Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads." +with open(path.join(here, 'README.rst'), encoding='utf-8') as f: + long_description = f.read() + setup( name = 'stringMLST', scripts = ['stringMLST.py'], - version = '0.3.6.2', + version = '0.3.6.3', description = 'Fast k-mer based tool for alignment and assembly-free multi locus sequence typing (MLST) directly from genome sequencing reads.', + long_description=long_description, author = 'Jordan Lab', author_email = 'pypi@atc.io', url = 'https://github.com/jordanlab/stringMLST', diff --git a/stringMLST.py b/stringMLST.py old mode 100755 new mode 100644 index 30b2e76..4fce5b6 --- a/stringMLST.py +++ b/stringMLST.py @@ -15,50 +15,232 @@ except ImportError: from urllib import urlopen, urlretrieve import argparse -version = """ stringMLST v0.3.6.2 (updated : March 18, 2017) """ +version = """ stringMLST v0.3.6.3 (updated : April 18, 2017) """ """ + +stringMLST free for academic users and requires permission before any commercial +use for any version of this code/algorithm. If you are a commercial user, please +contact king.jordan@biology.gatech.edu for permissions + LICENSE TERMS FOR stringMLST -1. INTENT/PURPOSE: -stringMLST is free for academic users and requires permission before any commercial use for -any version of this code/algorithm. -If you are a commercial user, please contact king.jordan@biology.gatech.edu for permissions. -2. LICENSEE: -Any person or organization who receives the software with a copy of this license. -3. INTELLECTUAL PROPERTY LICENSED: -The rights to use, copy, modify, and compile the software, -subject to the restrictions described in the present document. -5. SCOPE OF THE LICENSE -* NON-COMMERCIAL license for research and evaluation purposes ONLY. -* NO right to commercialize the software, or any derivative work, - without separate agreement with the copyright owners. -6. MODIFICATION -* License permits licensee to modify the software for their - research and evaluation purposes. -7. 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