Metadata-Version: 2.1
Name: junc_utils
Version: 0.5.2
Summary: Python programs for analyzing splicing junctions
Home-page: https://github.com/friend1ws/junc_utils
Author: Yuichi Shiraishi
Author-email: friend1ws@gamil.com
License: GPLv3
Description: # junc_utils
        
        [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
        [![Build Status](https://travis-ci.com/friend1ws/junc_utils.svg?branch=devel)](https://travis-ci.com/friend1ws/junc_utils.svg?branch=devel)
        
        Utility functions for analyzing splicing junction (generated by STAR, .SJ.out.tab files)
        
        ## Dependency
        
        ### Python
        `pysam`, [`annot_utils>=0.3.0`](https://github.com/friend1ws/annot_utils) packages.
        
        ### Software
        [htslib](http://www.htslib.org), [bedtools](http://bedtools.readthedocs.io/en/latest/)
        
        ## Install
        
        ```
        pip install junc_utils
        ```
        
        Alternatively, you can install from the source code
        ```
        wget https://github.com/friend1ws/junc_utils/archive/v0.5.0.tar.gz
        tar zxvf v0.5.0.tar.gz
        cd junc_utils-0.5.0
        python setup.py build install
        ```
        
        This package has been tested on Python 3.6, 3.7, 3.8, 3.9
        
        ## Commands
        
        ### fitler
        
        filter out splicing junctions outside specified conditions
        ```
        junc_utils filter [-h] [--read_num_thres READ_NUM_THRES]
                                 [--overhang_thres OVERHANG_THRES] [--keep_annotated]
                                 [--pooled_control_file POOLED_CONTROL_FILE]
                                 sample.SJ.out.tab output.txt
        ```
        
        ### annotate
        
        annotate splicing junctions
        
        ```
        junc_utils annotate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]
                                   [--junction_margin JUNCTION_MARGIN]
                                   [--exon_margin EXON_MARGIN]
                                   sample.SJ.out.tab output.txt
        ```
        
        ### merge_control
        
        merge, compress and index the splicing junction list
        
        ```
        junc_utils merge_control [-h] [--read_num_thres READ_NUM_THRES]
                                        [--overhang_thres OVERHANG_THRES]
                                        [--keep_annotated]
                                        [--sample_num_thres SAMPLE_NUM_THRES]
                                        junc_list.txt output_path
        ```
        
        ### associate
        
        associate junctions with mutations or SVs
        
        ```
        junc_utils associate [-h] [--grc] [--genome_id {hg19,hg38,mm10}]
                                    [--donor_size donor_size]
                                    [--acceptor_size acceptor_size]
                                    [--reference reference.fa] [--debug]
                                    [--mutation_format {vcf,anno}] [--only_dist]
                                    [--only_dist_search_margin only_dist_search_margin]
                                    [--sv] [--branchpoint]
                                    [--branchpoint_size branchpoint_size]
                                    annotated_junction.SJ.out.tab mutation.vcf.gz
                                    output_file
        ```
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: Unix
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Description-Content-Type: text/markdown
