diff --git a/transcript_structure/Outputs/csv_new.csv b/transcript_structure/Outputs/csv_new.csv
index 88a301674c9709792b1fa39ba3b721fb76dcf010..3dcf4bda7b86b89378ea50b4e2dd065194c8cb6a 100644
--- a/transcript_structure/Outputs/csv_new.csv
+++ b/transcript_structure/Outputs/csv_new.csv
@@ -1,8 +1,3 @@
Transcript_ID,Gene_ID,count
-1700034P13Rik-010,1700034P13Rik,3
-1700034P13Rik-100,1700034P13Rik,1
-1700034P13Rik-000,1700034P13Rik,1
-Rp1-111,Rp1,1
-Rp1-000,Rp1,2
-Rp1-010,Rp1,1
-Rp1-001,Rp1,1
+1700034P13Rik-111,1700034P13Rik,5
+Rp1-111,Rp1,5
diff --git a/transcript_structure/Outputs/gtf_new.gtf b/transcript_structure/Outputs/gtf_new.gtf
index e80579574e8088396d34b4d736efcbfaf8322d88..b710cb49d9579682c794ccb2b78d43cd3c1442b2 100644
--- a/transcript_structure/Outputs/gtf_new.gtf
+++ b/transcript_structure/Outputs/gtf_new.gtf
@@ -1,30 +1,6 @@
1 ensembl_havana gene 3999557 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-111"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
1 havana exon 4409170 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-111"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
-1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4351910 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "4"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-000"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
-1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4352202 4352081 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4290846 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-010"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana transcript 4290846 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; transcript_support_level "1";
-1 havana exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "1"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "2"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
-1 havana exon 4351910 4293012 . - . gene_id "ENSMUSG00000025900"; gene_version "12"; transcript_id "ENSMUST00000208793"; transcript_version "1"; exon_number "3"; gene_name "Rp1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "Rp1-001"; transcript_source "havana"; transcript_biotype "retained_intron"; exon_id "ENSMUSE00001379779"; exon_version "1"; transcript_support_level "1";
1 havana gene 9747648 9791924 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA";
-1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
-1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9752449 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-010"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
-1 havana exon 9747648 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-100"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
-1 havana exon 9747648 9748604 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9752449 9752564 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "2"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9789656 9789780 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "3"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
-1 havana exon 9791125 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "4"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-000"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
+1 havana transcript 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-111"; transcript_source "havana"; transcript_biotype "lncRNA"; transcript_support_level "1";
+1 havana exon 9747648 9791922 . + . gene_id "ENSMUSG00000097893"; gene_version "8"; transcript_id "ENSMUST00000181821"; transcript_version "7"; exon_number "1"; gene_name "1700034P13Rik"; gene_source "havana"; gene_biotype "lncRNA"; transcript_name "1700034P13Rik-111"; transcript_source "havana"; transcript_biotype "lncRNA"; exon_id "ENSMUSE00001104564"; exon_version "1"; transcript_support_level "1";
diff --git a/transcript_structure/cli.py b/transcript_structure/cli.py
new file mode 100644
index 0000000000000000000000000000000000000000..dfdc5c2d81f7a095482eb2c264f6ce58112c89d3
--- /dev/null
+++ b/transcript_structure/cli.py
@@ -0,0 +1,129 @@
+"""Command Line Interface for the transcript structure generator."""
+
+import argparse
+import logging
+import sys
+from enum import Enum
+
+from transcript_structure import __version__
+from transcript_structure.Generate_transcript_structure import BuildTranscriptStructure as bts
+
+LOG = logging.getLogger(__name__)
+
+
+class LogLevels(Enum):
+ """Log level enumerator."""
+
+ DEBUG = logging.DEBUG
+ INFO = logging.INFO
+ WARN = logging.WARNING
+ WARNING = logging.WARNING
+ ERROR = logging.ERROR
+ CRITICAL = logging.CRITICAL
+
+
+def parse_args() -> argparse.Namespace:
+ """Parse CLI arguments.
+
+ Returns:
+ Parsed CLI arguments.
+ """
+ # set metadata
+ description = (
+ f"{sys.modules[__name__].__doc__}\n\n"
+ ""
+ )
+ epilog = (
+ f"%(prog)s v{__version__}, (c) 2021 by Zavolab "
+ "(zavolab-biozentrum@unibas.ch)"
+ )
+
+ # instantiate parser
+ parser = argparse.ArgumentParser(
+ description=description,
+ epilog=epilog,
+ add_help=False,
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+ )
+
+ # add arguments
+ parser.add_argument(
+ 'input_gene_count',
+ type=str,
+ help="path and name of coma-separated file with gene abundances per gene",
+ )
+ parser.add_argument(
+ 'input_coordinates',
+ type=str,
+ help="path and name of gtf file with exon information about all genes",
+ )
+ parser.add_argument(
+ "--p_intron",
+ default=0,
+ type=float,
+ help="probability to include an intron",
+ )
+ parser.add_argument(
+ "csv_output_name",
+ type=str,
+ help="path and name of coma-separated file with count of differently spliced transcripts",
+ )
+ parser.add_argument(
+ "gtf_output_name",
+ type=str,
+ help="path and name of gtf file with intron coordinates of differently spliced transcripts",
+ )
+ parser.add_argument(
+ "--verbosity",
+ choices=[e.name for e in LogLevels],
+ default=LogLevels.INFO.name,
+ type=str,
+ help="logging verbosity level",
+ )
+
+ # return parsed arguments
+ return parser.parse_args()
+
+
+def setup_logging(verbosity: str = 'INFO') -> None:
+ """Configure logging.
+
+ Args:
+ verbosity: Level of logging verbosity.
+ """
+ level = LogLevels[verbosity].value
+ logging.basicConfig(
+ level=level,
+ format="[%(asctime)s %(levelname)s] %(message)s",
+ datefmt='%Y-%m-%d %H:%M:%S',
+ )
+
+
+def main() -> None:
+ """Entry point for CLI executable."""
+ try:
+ # handle CLI args
+ args = parse_args()
+
+ # set up logging
+ setup_logging(verbosity=args.verbosity)
+ LOG.info("Started transcript structure builder...")
+ LOG.debug(f"CLI arguments: {args}")
+
+ builder = bts(input_gene_count=args.input_gene_count,
+ input_coordinates=args.input_coordinates,
+ p_intron=args.p_intron)
+ builder.generate_transcript_structure()
+ builder.write_csv(args.csv_output_name)
+ builder.write_gtf(args.gtf_output_name)
+
+ except KeyboardInterrupt:
+ LOG.error('Execution interrupted.')
+ sys.exit(128 + signal.SIGINT)
+
+ # conclude execution
+ LOG.info("Done.")
+
+
+if __name__ == '__main__':
+ main()