diff --git a/scripts/match_reprtranscript_expressionlevel.py b/scripts/match_reprtranscript_expressionlevel.py
index 547df014f2001bd695659b1e5189e930d45476bc..1599b7c33212e11ea0dedf0fbeac70d593fdfe3c 100644
--- a/scripts/match_reprtranscript_expressionlevel.py
+++ b/scripts/match_reprtranscript_expressionlevel.py
@@ -1,3 +1,4 @@
+### Made by Hugo Gillet ###
import pandas as pd
import json
import re
@@ -5,7 +6,7 @@ import representative as repr
import os
-def dict_reprTrans_to_df(dict_reprTrans: dict[str,str])-> pd.DataFrame:
+def dict_reprTrans_to_df(dict_reprTrans: dict[str, str]) -> pd.DataFrame:
"""Convert a dictionary of genes and their representative transcript into a dataframe
@@ -22,17 +23,21 @@ def dict_reprTrans_to_df(dict_reprTrans: dict[str,str])-> pd.DataFrame:
"""
pass
- if not type(dict_reprTrans) is dict :
+ if not type(dict_reprTrans) is dict:
raise TypeError("Only dict are allowed")
- if type(list(dict_reprTrans.keys())[0]) is not str :
+ if type(list(dict_reprTrans.keys())[0]) is not str:
raise TypeError("Key should be strings")
- if type(list(dict_reprTrans.values())[0]) is not str :
+ if type(list(dict_reprTrans.values())[0]) is not str:
raise TypeError("Values should be strings")
- df_reprTrans = pd.DataFrame.from_dict(dict_reprTrans, orient="index", columns=["reprTranscript"])
+ df_reprTrans = pd.DataFrame.from_dict(
+ dict_reprTrans, orient="index", columns=["reprTranscript"]
+ )
df_reprTrans = df_reprTrans.reset_index(level=0)
- df_reprTrans.columns = ["Gene", 'reprTrans']
- df_reprTrans["reprTrans"] = df_reprTrans["reprTrans"].str.replace(r'\.[1-9]', '', regex=True)
+ df_reprTrans.columns = ["Gene", "reprTrans"]
+ df_reprTrans["reprTrans"] = df_reprTrans["reprTrans"].str.replace(
+ r"\.[1-9]", "", regex=True
+ )
return df_reprTrans
@@ -51,13 +56,12 @@ def txt_to_dict(dict_txt: str) -> dict:
"""
pass
- input : str = open(dict_txt, "r").read()
- input : str = input.replace("\'", "\"")
+ input: str = open(dict_txt, "r").read()
+ input: str = input.replace("'", '"')
dict = json.loads(input)
return dict
-
def transcripts_by_gene_inDf(df_gtfSelection: pd.DataFrame) -> pd.DataFrame:
"""Convert multiindex dataframe from function into a simple dataframe
@@ -77,12 +81,14 @@ def transcripts_by_gene_inDf(df_gtfSelection: pd.DataFrame) -> pd.DataFrame:
pass
df_gene = df_gtfSelection.set_index(["Gene"])
df_gene = df_gene.drop(columns=["Support_level"])
- df_gene['Transcript']=df_gene['Transcript'].str.replace(r"\.[0-9]","", regex=True)
+ df_gene["Transcript"] = df_gene["Transcript"].str.replace(
+ r"\.[0-9]", "", regex=True
+ )
df_gene = df_gene.reset_index(level=0)
return df_gene
-def tsv_or_csv_to_df(input_txt:str) -> pd.DataFrame :
+def tsv_or_csv_to_df(input_txt: str) -> pd.DataFrame:
"""Convert tsv or csv file into a pandas dataframe
Args:
@@ -96,13 +102,19 @@ def tsv_or_csv_to_df(input_txt:str) -> pd.DataFrame :
None
"""
pass
- df_input =pd.read_csv(input_txt, sep=r"[\t,]", lineterminator='\n',
- names=["Transcript", "Expression_level"],
- engine = "python")
+ df_input = pd.read_csv(
+ input_txt,
+ sep=r"[\t,]",
+ lineterminator="\n",
+ names=["Transcript", "Expression_level"],
+ engine="python",
+ )
return df_input
-def exprLevel_byGene(df_exprTrasncript:pd.DataFrame, df_output_gtf_selection:pd.DataFrame) -> pd.DataFrame :
+def exprLevel_byGene(
+ df_exprTrasncript: pd.DataFrame, df_output_gtf_selection: pd.DataFrame
+) -> pd.DataFrame:
"""find the gene of each transcipt given by the expression level csv/tsv file,
and summ expression level of all transcipts from the same gene.
@@ -118,12 +130,19 @@ def exprLevel_byGene(df_exprTrasncript:pd.DataFrame, df_output_gtf_selection:pd.
Raises:
None
"""
- pass
- df_merged = pd.merge(df_output_gtf_selection, df_exprTrasncript , how="inner", on="Transcript")
- df_sum = df_merged.groupby("Gene").sum("Expression_level") # sum transcripts comming from the same gene
+ pass
+ df_merged = pd.merge(
+ df_output_gtf_selection, df_exprTrasncript, how="inner", on="Transcript"
+ )
+ df_sum = df_merged.groupby("Gene").sum(
+ "Expression_level"
+ ) # sum transcripts comming from the same gene
return df_sum
-def match_byGene(df_reprTranscript: pd.DataFrame, df_expressionLevel_byGene:pd.DataFrame) -> pd.DataFrame:
+
+def match_byGene(
+ df_reprTranscript: pd.DataFrame, df_expressionLevel_byGene: pd.DataFrame
+) -> pd.DataFrame:
"""Find matching genes bewteen the 2 args
Args:
@@ -141,13 +160,16 @@ def match_byGene(df_reprTranscript: pd.DataFrame, df_expressionLevel_byGene:pd.D
Raises:
None
"""
- pass
- df_merged = pd.merge(df_reprTranscript, df_expressionLevel_byGene , how="outer", on="Gene")
+ pass
+ df_merged = pd.merge(
+ df_reprTranscript, df_expressionLevel_byGene, how="outer", on="Gene"
+ )
df_clean = df_merged.dropna(axis=0)
- df_clean = df_clean.loc[:, ["reprTrans","Expression_level"]]
+ df_clean = df_clean.loc[:, ["reprTrans", "Expression_level"]]
return df_clean
-def output_tsv(dataframe: pd.DataFrame)-> pd.DataFrame :
+
+def output_tsv(dataframe: pd.DataFrame) -> pd.DataFrame:
"""Convert pandas dataframe into a tsv file
Args:
@@ -161,15 +183,23 @@ def output_tsv(dataframe: pd.DataFrame)-> pd.DataFrame :
Raises:
None
"""
- pass
+ pass
- csv_file = dataframe.to_csv(os.getcwd()+"\ReprTrans_ExpressionLevel.tsv", sep="\t",
- index=False, header=False)
+ csv_file = dataframe.to_csv(
+ os.getcwd() + "\ReprTrans_ExpressionLevel.tsv",
+ sep="\t",
+ index=False,
+ header=False,
+ )
return csv_file
+
### functions to run this part of the programm
-def match_reprTranscript_expressionLevel(exprTrans:str, dict_reprTrans:dict, intermediate_file:str):
+
+def match_reprTranscript_expressionLevel(
+ exprTrans: str, dict_reprTrans: dict, intermediate_file: str
+):
"""Combine functions to replace transcripts from an expression level csv/tsv file
with representative transcripts
@@ -199,14 +229,5 @@ def match_reprTranscript_expressionLevel(exprTrans:str, dict_reprTrans:dict, int
# run the programm
-#dict_txt = a #input a dict of {gene:reprTrans} in the form of a txt file
-#input_intermediate_file = b #input the intermediate file generated by transckript extractor
-#input_expr = c #input a csv or tsv file containing the expr level
-
-#dict_reprTrans = txt_to_dict(dict_txt)
-#match_final = match_reprTranscript_expressionLevel(input_expr, dict_reprTrans, input_intermediate_file)
-#print("this is the function :\n\n {}".format(match_final))
-
-if __name__ == "__main__":
+if __name__ == "__main__":
match_reprTranscript_expressionLevel()
-