athos / fusion_utils

utility for comparing fusion results

fusion_utils

Introduction

fusion_utils is a software for processing the result of fusionfusion.

Dependency

Python

Python (>= 2.7), pysam (>= 0.8.1),annot_utils packages.

Software

bedtools

Install

git clone https://github.com/friend1ws/fusion_utils.git
cd fusion_utils
python setup.py build install

Commands

comp

Compare results of fusion calls (by fusionfusion, STAR-fusion, Tophat-fusion, MapSplice2, Genomon-Fusion) or SV calls (by GenomonSV).

fusion_utils comp [-h] [--margin MARGIN]
                       [--sv_margin_major SV_MARGIN_MAJOR]
                       [--sv_margin_minor SV_MARGIN_MINOR]
                       fusion1.txt
                       {fusionfusion,fusionfusion_part,genomonSV,star_fusion,genomon_fusion,mapsplice2,tophat_fusion}
                       fusion2.txt
                       {fusionfusion,fusionfusion_part,genomonSV,star_fusion,genomon_fusion,mapsplice2,tophat_fusion}
                       output.txt

rmdup

Remove putative duplicates from results of fusion calls.

fusion_utils rmdup [-h]
                   [--type {fusionfusion,fusionfusion_part,genomonSV,star_fusion,genomon_fusion,mapsplice2,tophat_fusion}]
                   fusion.txt output.txt

filt

Filter out unreliable candidates the results of fusion calls.

fusion_utils filt [-h]
                   [--type {fusionfusion,fusionfusion_part,star_fusion,genomon_fusion,mapsplice2,tophat_fusion}]
                   [--grc] [--genome_id {hg19,hg38,mm10}]
                   [--thres threshould] [--filter_same_gene]
                   [--filter_unspliced]
                   fusion.txt output.txt