add: command line interface

transcript_structure/Outputs/csv_new.csv

 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

transcript_structure/Outputs/gtf_new.gtf

 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"; 

transcript_structure/cli.py

+"""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()