Metadata-Version: 2.1
Name: dart_id
Version: 2.0.2
Summary: RT Alignment and Peptide ID Confidence Updating for LC-MS/MS Data
Home-page: https://github.com/SlavovLab/DART-ID
Author: Albert Chen
Author-email: chen.alb@husky.neu.edu
License: MIT
Project-URL: Documentation, https://github.com/SlavovLab/DART-ID
Project-URL: Source, https://github.com/SlavovLab/DART-ID
Project-URL: Tracker, https://github.com/SlavovLab/DART-ID/issues
Project-URL: Lab Page, https://web.northeastern.edu/slavovlab/
Description: # DART-ID
        
        Website: [https://slavovlab.github.io/DART-ID/](https://slavovlab.github.io/DART-ID/)
        
        Manuscript: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3)
        
        ----------
        
        ## Getting started
        
        ### Dependencies
        
        DART-ID requires Python >= 3.4, and has been tested on Windows 8 / OSX Mojave 10.14 / Centos 7 / Ubuntu 14.04.
        
        ### Installation
        
        ```bash
        pip install dart-id
        ```
        
        ### Usage
        
        DART-ID requires a YAML-formatted configuration file to run. An example annotated config file can be found in [example/config_annotated.yaml](https://github.com/SlavovLab/DART-ID/blob/master/example/config_annotated.yaml). You can specify input files and the output folder on the command line, if that's what you prefer.
        
        View the command-line arguments anytime by running: ```dart_id -h```.
        
        ```
        usage: dart_id [-h] [-i INPUT [INPUT ...]] [-o OUTPUT] [-v] [--version] -c
                         CONFIG_FILE
        
        optional arguments:
          -h, --help            show this help message and exit
          -i INPUT [INPUT ...], --input INPUT [INPUT ...]
                                Input file(s) from search engine output (e.g.,
                                MaxQuant evidence.txt). Not required if input files
                                are specified in the config file
          -o OUTPUT, --output OUTPUT
                                Path to output folder
          -v, --verbose
          --version             Display the program's version
          -c CONFIG_FILE, --config-file CONFIG_FILE
                                Path to config file (required). See
                                example/config_example.yaml
        ```
        
        ### Example runs
        
        An example configuration file can be downloaded from GitHub: [https://github.com/SlavovLab/DART-ID/blob/master/config_files/example_sqc_67_95_varied.yaml](https://github.com/SlavovLab/DART-ID/blob/master/config_files/example_sqc_67_95_varied.yaml).
        
        The first few lines of the above configuration file specify the path to the input file:
        
        ```yaml
        ## Input
        ## ==========================
        
        input: 
          - /path/to/SQC_67_95_Varied/evidence.txt
        ```
        
        You can download the ```evidence.txt``` file from MassIVE: [ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt](ftp://massive.ucsd.edu/MSV000083149/other/MaxQuant/SQC_67_95_Varied/evidence.txt). 
        
        Then edit the path to the file downloaded, and run the following command:
        
        ```bash
        dart_id -c config_files/example_sqc_67_95_varied.yaml -o ~/DART_ID/SQC_67_95_varied_20181206
        ```
        
        The ```-o``` parameter points to the output folder for DART-ID. You can also specify this path in the config file.
        
        An example analysis of the data and configuration file specified above is available publicly at [ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/](ftp://massive.ucsd.edu/MSV000083149/other/Alignments/SQC_varied_20180711_4/). 
        
        ---
        
        ## About the project
        
        DART-ID is a project developed in the [Slavov Laboratory](https://web.northeastern.edu/slavovlab/) at [Northeastern University](https://www.northeastern.edu/) [Bioengineering](http://www.bioe.neu.edu/), and was authored by [Albert Tian Chen](https://atchen.me), [Alexander Franks](http://afranks.com/) (of [UCSB Statistics and Applied Probability](https://www.pstat.ucsb.edu/)), and [Nikolai Slavov](https://web.northeastern.edu/slavovlab/).
        
        The manuscript for this tool is available on bioRxiv: [https://www.biorxiv.org/content/10.1101/399121v3](https://www.biorxiv.org/content/10.1101/399121v3).
        
        Contact the authors by email: [nslavov\{at\}northeastern.edu](mailto:nslavov@northeastern.edu).
        
        ### License
        
        DART-ID is distributed by an [MIT license](https://github.com/SlavovLab/DART-ID/blob/master/LICENSE.txt).
        
        ### Contributing
        
        Please feel free to contribute to this project by opening an issue or pull request in the [GitHub repository](https://github.com/SlavovLab/DART-ID).
        
        ### Data
        
        All data used for the manuscript is available on [UCSD's MassIVE Repository](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=ed5a1ab37dc34985bbedbf3d9a945535)
        
        ### Figures/Analysis
        
        Scripts for the figures in the DART-ID manuscript are available in a separate GitHub repository, [https://github.com/SlavovLab/DART-ID_2018](https://github.com/SlavovLab/DART-ID_2018) 
Keywords: bayesian retention time psm peptide spectra update
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
