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
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