From 24d3533232e996480bfa601549b841117841e7fa Mon Sep 17 00:00:00 2001
From: Larissa Glass <larissa.glass@unibas.ch>
Date: Tue, 1 Nov 2022 16:06:34 +0000
Subject: [PATCH] Draf: Resolve "Input/output"
---
README.md | 13 +++++++++++++
src/__init__.py | 3 +++
src/main.py | 17 +++++++++++++++++
3 files changed, 33 insertions(+)
create mode 100644 src/__init__.py
create mode 100644 src/main.py
diff --git a/README.md b/README.md
index 3161d7a..58cfa03 100644
--- a/README.md
+++ b/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
diff --git a/src/__init__.py b/src/__init__.py
new file mode 100644
index 0000000..d9744d3
--- /dev/null
+++ b/src/__init__.py
@@ -0,0 +1,3 @@
+"""Transcript structure generator package."""
+
+__version__ = '0.0.0'
\ No newline at end of file
diff --git a/src/main.py b/src/main.py
new file mode 100644
index 0000000..ea1a4d9
--- /dev/null
+++ b/src/main.py
@@ -0,0 +1,17 @@
+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
--
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