From 34841faddfc3c8f664bedc7ab6a45f2d4cf1dcec Mon Sep 17 00:00:00 2001
From: Hugo Gillet <hugo.gillet@stud.unibas.ch>
Date: Sun, 4 Dec 2022 23:45:10 +0000
Subject: [PATCH] Update representative.py
---
scripts/representative.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/scripts/representative.py b/scripts/representative.py
index a670ad6..fcc7bf8 100644
--- a/scripts/representative.py
+++ b/scripts/representative.py
@@ -1,5 +1,6 @@
import pandas as pd
+import os
'''
This part of the code take as input a gtf modified file
@@ -62,7 +63,7 @@ def representative_transcripts_inDict(df_gtfSelection: pd.DataFrame) -> pd.DataF
df_multIndex = df_gtfSelection.set_index(["Gene", "Transcript"])
#highest support level = 1 , worst = 5, NA = 100
- df_min = df_multIndex.groupby(level=["Gene"])["Support_level"].transform("min")
+ df_min = df_multIndex[df_multIndex["Support_level"] == df_multIndex["Support_level"].min()]
df_final = df_min.reset_index(level = "Transcript")
df_final = df_final.drop(columns = ["Support_level"])
dict_representative_transcripts = df_final.groupby("Gene")["Transcript"].apply(list).to_dict()
@@ -70,7 +71,7 @@ def representative_transcripts_inDict(df_gtfSelection: pd.DataFrame) -> pd.DataF
-def find_repr_by_SupportLevel(intermediate_file : str) -> dict[str,str]:
+def find_repr_by_SupportLevel(intermediate_file: str) -> dict[str,str]:
"""Combine functions import_gtfSelection_to_df()
and representative_transcripts_inDict()
@@ -93,4 +94,4 @@ def find_repr_by_SupportLevel(intermediate_file : str) -> dict[str,str]:
if __name__ == "__main__":
- find_repr_by_SupportLevel()
+ find_repr_by_SupportLevel()
--
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