Transcript Intersect & Merge, or T.I.M for short, is a tool to discover IGRs (InterGenic Regions) in Bacteria. It uses a transcriptome assembly mapped to a reference genome and the annotation of said genome to find features in the transcriptome assembly not found in and not intersecting with annotations in the reference genome.

Needed Arguments:
--assembly A The mapped assembly in gff format (filepath from pwd or absolute)
--genome G The annotated reference genome in gff3 format (filepath from pwd or absolute)
--output_path O Path of the output files (filepath from pwd or absolute)
--project_prefix N Project name, all output files will be prefixed with this

Optional Arguments:
--help, -h show this help message and exit
--ss N Should features only be excluded, if the intersection occurs on their strand? 1= Yes 0=No (Default:0)
--distance D Distance of kept feature to annotated features
--merge M Should non-intersecting features be merged to the first feature of the merge? 0= Yes 1=No (Default:0)

Example Command: python3 TIM.py --assembly test_data/Assembly.gff3 --genome test_data/Genome.gff3 --distance 10

The Input Files have to be gff3 files with the following column order: 'seqid', 'source', 'type', 'start', 'stop', 'score', 'strand', 'phase', 'attributes'. While the names are hardcoded, the order of columns may be changed in line 45 of the TIM.py script.