Junctions Comparer
A simple Python tool to compare junctions across several samples
#Usage
usage: junctions_comparer.py [-h] [-nb | -q] [-n MIN_READS] [-t TEMP_DIR]
[-o OUT_DIR] [-r RESULTS_FILE]
[-rl RESULTS_DELIMITER] [-u UNKNOWN_ID]
[-gl GENE_DELIMITER] [-a {stranded,unstranded}]
gtf_file bed_file bed_file [bed_file ...]
Arguments
positional arguments:
gtf_file reference annotation file in GTF format
bed_file junction annotation file in BED format
Options
optional arguments:
-h, --help show this help message and exit
-nb, --no-bars disables loading bars (use when redirecting output to
file)
-q, --quiet
-n MIN_READS, --min-reads MIN_READS
minimum number of reads supporting junction to pass
filter (default: 3)
-t TEMP_DIR, --temp-dir TEMP_DIR
directory where to keep temporary files (default:
sj_tmp)
-o OUT_DIR, --out-dir OUT_DIR
directory where to keep output files (default: sj_out)
-r RESULTS_FILE, --results-file RESULTS_FILE
name for final result file (default: results.csv)
-rl RESULTS_DELIMITER, --results-delimiter RESULTS_DELIMITER
delimiter for output CSV file (default: ,)
-u UNKNOWN_ID, --unknown-id UNKNOWN_ID
name for unknown genes (default: UNKNOWN)
-gl GENE_DELIMITER, --gene-delimiter GENE_DELIMITER
delimiter for gene lists in output (default: |)NOTE:
MUST NOT BE THE SAME AS -rl
-a {stranded,unstranded}, --analysis {stranded,unstranded}
type of analysis (default: unstranded)