Metadata-Version: 2.1
Name: barseq
Version: 1.0.1
Summary: Analysis of barseq data.
Home-page: https://github.com/mjmlab/barseq
Author: Emanuel Burgos
Author-email: eburgos@wisc.edu
License: BSD
Description: [![Build Status](https://travis-ci.com/eburgoswisc/barseq.svg?branch=master)](https://travis-ci.com/eburgoswisc/barseq)
        ![Python 3.7](https://img.shields.io/badge/python-3.7-blue.svg)
        
        # barseq 
        
        Python package for analyzing barseq data.
        
        ### Installation
        
        ```bash
        pip install git+https://github.com/mjmlab/barseq.git@master
        ``` 
        
        ### Usage
        
        ```bash
        barseq -i <directory of sequencing reads> -b <barcode file> -e <experiment name>
        ```
        
        `-i` / `--input`
        
        - Directory with Illumina reads in either fastq or fastq.gz.
        
        
        `-b` / `--barcodes`
        
        - CSV file with barcode and correspondent gene names.
        
        
        `-e` / `--experiment`
        
        - Name of experiment, it is used for creating results folder.
        
        ### Files Needed
        
        **Directory of Illumina reads [`-i`]** for analyzing. Can be either fastq or fastq.gz format
        
        ```text
        @M06026:87:000000000-D69HY:1:1102:15909:1336 1:N:0:TGACCA
        CTCTAGAAAGTATAGGAACTTCAGGGCCATTTATATACCTTCCACTCTTCAACCGTGTCTTGACTTGACCTGGATGTCTCTACTGCTGTCATGCTACGTAGCTCATGCTACGTCGATCTAGTCGATGCATGCTAGCTGATCGACTCTCTTC
        +
        A#>>>3AA2DD>FBFGBFBFBFDDFGGAAEEEHDHFFFDDDBDGDFDDDDDADFGFFDDBFFEBFD5DFEEBBADABFGFGBBFGDD5BF3F43B3F1/11B144BGEBF@BBFB0B0BBFBBBBBBBB?E/FGFBB?/???B???/?FGG
        ```
        
        **Barcode file [`-b`]** with gene names. Needs to be in CSV format.
        
        ```text
        Barcode,Gene
        ATGAAGACTGTTGCCGTA,WT
        CACGACGCCCTCCGCGGA,gene1
        ACTATTACGCAAAATAAT,gene2
        ATGGAAGATATTATTATT,gene3
        CCTCTCCAACCGGGTCTG,gene4
        CCCGGTCGCCTAGCCCCG,gene5
        GGCCCCCCGCCCGTCCCC,gene6
        GGATCACTGCTAGCGTAT,gene7
        CCTGCAGCAGCGGCCCGC,gene8
        ACACATGCAGACATAGAG,gene9
        CGCGCCATCCGCCGCCCA,gene10
        AATATTCAGATGGGACGT,gene11
        ```
        
        ### Output
        
        #### `results/` directory
        
        - <experiment>_results.csv: barcode counts found in each sequence file.
        
        
        | Gene |       Barcode        | Sample 1 | Sample 2 | Sample 3 | ... |
        | ---- | -------------------- | --------:| --------:| --------:| --- |
        | gene1| `ATGAAGACTGTTGCCGTA` |    500   |    5     |     7    | ... |
        | gene2| `CACGACGCCCTCCGCGGA` |     12   |   13     |    19    | ... |
        | gene3| `ACTATTACGCAAAATAAT` |     13   |   11     |    10    | ... |
        |_other|        _other        |     28   |   40     |    29    | ... |
        
        
        
        ### Barseq Workflow
        
        ![barseq_diagram](docs/barseq_workflow.png)
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: MacOS X
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
