feat: add cli, setup.py

Added and refactored new_exe.py into cli.py, added setup.py, requirements.txt, requirements_dev.txt. CLI is now executable, CLI arguments available and can be successfully executed with -h option.

transcript_sampler/cli.py

@@ -2,92 +2,81 @@
 import argparse
 import time
 import logging
-from find_reptrans import FindRepTrans
-from match_reptrans_explvl import MatchReptransExplvl
-from poisson_sampling import SampleTranscript
-
-find_rep_trans = FindRepTrans()
-match_reptrs_explvl = MatchReptransExplvl()
-poisson_sample = SampleTranscript()
 
 logging.basicConfig(
     format='[%(asctime)s: %(levelname)s] %(message)s \
         (module "%(module)s")',
     level=logging.INFO,
-)
-LOG = logging.getLogger("main")
-
-
-def main(args: argparse.Namespace):
-    """Execute transcript sampler."""
-    start = time.time()
-    LOG.info("Started transcript sampler...")
-    dict_repr_trans = find_rep_trans.get_rep_trans(args.input_gtf)
-    df_repr = match_reptrs_explvl.match_repr_transcript_expression_level(
-        dict_reprTrans=dict_repr_trans,
-        exprTrans=args.input_csv,
-        gtf_file=args.input_gtf
-        )
-    LOG.info(
-        "Finding match between representative transcripts \
-            and expression level file"
-        )
-    LOG.info("Poisson sampling of transcripts")
-    poisson_sample.transcript_sampling(
-        args.transcript_nr, df_repr, args.output_csv)
-    LOG.info("Output CSV file ready")
-
-    LOG.info("Writing output GTF file")
-    find_rep_trans.gtf_file_writer(
-        args.input_gtf, dict_repr_trans, args.output_gtf)
+    )
 
-    end = time.time()
-    LOG.info("Script executed in %s sec", (end - start))
+from transcript_sampler.find_reptrans import FindRepTrans  # noqa: E402,E501 # pylint:disable=wrong-import-position
+from transcript_sampler.match_reptrans_explvl import MatchReptransExplvl  # noqa: E402,E501 # pylint:disable=wrong-import-position
+from transcript_sampler.poisson_sampling import SampleTranscript  # noqa: E402,E501 # pylint:disable=wrong-import-position
 
+find_rep_trans = FindRepTrans()
+match_reptrs_explvl = MatchReptransExplvl()
+poisson_sample = SampleTranscript()
 
-def parse_arguments() -> argparse.Namespace:
-    """Request parameters from user on CLI.
 
-    Returns:
-        argparse.Namespace: object of arguments from CLI.
-    """
+def main():
+    """Execute transcript sampler."""
     parser = argparse.ArgumentParser(
         description="Transcript sampler",
         formatter_class=argparse.ArgumentDefaultsHelpFormatter,
     )
     parser.add_argument(
-        "--input_gtf", required=True,
+        "--input_gtf", required=True, default=None,
         help="GTF file with genome annotation"
         )
     parser.add_argument(
-        "--input_csv", required=True,
+        "--input_csv", required=True, default=None,
         help="CSV or TSV file with transcripts and their expression level"
         )
     parser.add_argument(
-        "--output_gtf", required=True,
+        "--output_gtf", required=True, default=None,
         help="Output path for the new GTF file of representative transcripts"
         )
     parser.add_argument(
-        "--output_csv", required=True,
+        "--output_csv", required=True, default=None,
         help="Output path for the new CSV file of representative transcripts \
             and their sampled number"
         )
     parser.add_argument(
-        "--n_to_sample", required=True,
+        "--n_to_sample", required=True, default=None,
         help="Total number of transcripts to sample"
         )
     args = parser.parse_args()
 
-    return args
+    log = logging.getLogger("main")
+    start = time.time()
+    log.info("Started transcript sampler...")
+    dict_repr_trans = find_rep_trans.get_rep_trans(args.input_gtf)
+    df_repr = match_reptrs_explvl.match_repr_transcript_expression_level(
+        dict_reprTrans=dict_repr_trans,
+        exprTrans=args.input_csv,
+        gtf_file=args.input_gtf
+        )
+    log.info(
+        "Finding match between representative transcripts \
+            and expression level file"
+        )
+    log.info("Poisson sampling of transcripts")
+    poisson_sample.transcript_sampling(
+        args.n_to_sample, df_repr, args.output_csv)
+    log.info("Output CSV file ready")
 
+    log.info("Writing output GTF file")
+    find_rep_trans.gtf_file_writer(
+        args.input_gtf, dict_repr_trans, args.output_gtf)
 
-if __name__ == '__main__':
+    end = time.time()
+    log.info("Script executed in %s sec", (end - start))
+
+
+if __name__ == "__main__":
     logging.basicConfig(
         format='[%(asctime)s: %(levelname)s] %(message)s \
             (module "%(module)s")',
         level=logging.INFO,
-    )
-    logger = logging.getLogger(__name__)
-
-    arguments = parse_arguments()
-    main(arguments)
+        )
+    main()