junc_utils

Utility functions for analyzing splicing junction (generated by STAR, .SJ.out.tab files)

Dependency

Python

pysam, annot_utils>=0.3.0 packages.

Software

htslib, bedtools

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