Metadata-Version: 2.1
Name: chimera-utils
Version: 0.6.0rc1
Summary: Python tools for processing chimeric reads and lists of gene fusions.
Home-page: https://github.com/friend1ws/chimera_utils
Author: Yuichi Shiraishi
Author-email: friend1ws@gamil.com
License: GPLv3
Description: # chimera_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.org/friend1ws/chimera_utils.svg?branch=devel)](https://travis-ci.org/friend1ws/chimera_utils)
        
        
        ## Introduction 
        
        This is a suite of tools for processing chimeric reads generated at a STAR alignment step (Chimeric.out.sam files).
        
        ## Dependency
        
        ### Python
        Python (>= 2.7), pysam, [annot_utils](https://github.com/friend1ws/annot_utils), [fusionfusion](https://github.com/Genomon-Project/fusionfusion)
        
        ### Software
        [htslib](http://www.htslib.org), [bedtools](http://bedtools.readthedocs.io/en/latest/)
        
        
        ## Install
        
        ```
        pip install chimera_utils
        ```
        
        Alternatively you can download from the source code:
        ```
        wget https://github.com/friend1ws/chimera_utils/archive/v0.5.0.tar.gz
        tar zxvf v0.5.0.tar.gz
        cd chimera_utils-0.5.0
        python setup.py build install
        ```
        
        For the last command, you may need to add --user if using a shared computing cluster.
        
        ## Commands
        
        ### count
        Count supporting read pairs for each chimera junction
        
        ```
        chimera_utils count [-h] [--abnormal_insert_size ABNORMAL_INSERT_SIZE]
                                  [--min_major_clipping_size MIN_MAJOR_CLIPPING_SIZE]
                                  [--min_read_pair_num MIN_READ_PAIR_NUM]
                                  [--min_cover_size MIN_COVER_SIZE]
                                  [--anchor_size_thres ANCHOR_SIZE_THRES]
                                  [--min_chimeric_size MIN_CHIMERIC_SIZE] [--debug]
                                  Chimeric.out.sam output_file
        ```
        
        ### merge_control
        Merge chimeric junction cout file (generated by `count` command) of control data (typically) for later filtering
        
        ```
        chimera_utils merge_control [-h] chimeric_count_list.txt output_file
        ```
        
        ### associate
        Associate chimeric junctions with the output of GenomonSV
        
        ```
        chimera_utils associate [-h] [--margin MARGIN]
                                       [--sv_margin_major SV_MARGIN_MAJOR]
                                       [--sv_margin_minor SV_MARGIN_MINOR]
                                       [--genome_id {hg19,hg38,mm10}] [--grc]
                                       [--debug]
                                       chimera.txt genomonSV.result.txt output.txt
        ```
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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
