Draf: Resolve "Input/output"

README.md

@@ -7,3 +7,16 @@ conda env create --file environment.yml
 conda activate transcript-structure-generator
 ```
 
+# Usage
+
+Input:
+- Csv-formatted file ("ID,Count") with counts for individual transcripts
+- Probability of intron inclusion (float in range [0,1])
+- gtf-formatted file with exon coordinates of the transcripts included in the csv file
+
+Output:
+- gtf-formatted file containing generated intron/exon structures per transcript
+- csv-formatted file ("NewTranscriptID,ID,Count") with
+	- id of generated transcript
+	- id of original transcript (without intron inclusions)
+	- count
\ No newline at end of file

src/__init__.py

+"""Transcript structure generator package."""
+
+__version__ = '0.0.0'
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src/main.py

+import argparse
+from pathlib import Path
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--transcripts", type=str)
+    parser.add_argument("--annotation", type=str)
+    parser.add_argument("--prob_inclusion", type=float)
+    args = parser.parse_args()
+
+    input_transcripts_file = args.transcripts
+    input_annotations_file = args.annotation
+    prob_inclusion = args.prob_inclusion
+    input_transcripts_path = Path(input_transcripts_file)
+    input_annotations_path = Path(input_annotations_file)
+    output_transcripts_file = "generated_" + input_transcripts_path.stem + ".csv"
+    output_annotations_file = "generated_" + input_annotations_path.name