From d1b17ada3387fd147970cd175f87ef6c7cb63df4 Mon Sep 17 00:00:00 2001
From: Jakob Rien <jakobj.rien@stud.unibas.ch>
Date: Tue, 13 Dec 2022 08:38:48 +0000
Subject: [PATCH] Replace poisson_sampling.py
---
scripts/poisson_sampling.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/scripts/poisson_sampling.py b/scripts/poisson_sampling.py
index 60d043d..fedd8e8 100644
--- a/scripts/poisson_sampling.py
+++ b/scripts/poisson_sampling.py
@@ -1,7 +1,14 @@
+### Called Packages ###
import pandas as pd
import numpy as np
import argparse
+import transcript_extractor as te
+
+python_version = "3.7.13"
+module_list =[pd,np,argparse]
+modul_name_list = ["pd","np","argparse"]
+### Functions ###
'''
Sample transcript
@@ -16,11 +23,13 @@ output: csv file with gene id and count
'''
-def transcript_sampling(total_transcript_number, csv_file, output_csv):
- df = pd.read_csv(csv_file, sep='\t', lineterminator='\n', names=["id", "level"])
+def transcript_sampling(total_transcript_number, df_repr, output_csv):
+ #df = pd.read_csv(csv_file, sep="\t", lineterminator="\n", names=["id", "level"])
+ df = df_repr # the function "match_reprTranscript_expressionLevel()" now directly output a dataframe
levels = []
sums = df['level'].tolist()
total = sum(sums)
+ total_transcript_number=int(total_transcript_number) # I added this because writting a number in the terminal inputed a string
normalized = total_transcript_number/total
for expression_level in df['level']:
poisson_sampled = np.random.poisson(expression_level*normalized)
@@ -30,6 +39,7 @@ def transcript_sampling(total_transcript_number, csv_file, output_csv):
pd.DataFrame.to_csv(transcript_numbers, output_csv)
if __name__ == '__main__':
+ #te.version_control(module_list,modul_name_list,python_version)
parser = argparse.ArgumentParser(
description="Transcript Poisson sampler, csv output",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
--
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