From 05453696c0958bce151870e324b0f8e22bf8a210 Mon Sep 17 00:00:00 2001
From: Jakob Rien <jakobj.rien@stud.unibas.ch>
Date: Tue, 13 Dec 2022 08:38:31 +0000
Subject: [PATCH] Replace new_exe.py
---
scripts/new_exe.py | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/scripts/new_exe.py b/scripts/new_exe.py
index aaf61af..7020547 100644
--- a/scripts/new_exe.py
+++ b/scripts/new_exe.py
@@ -1,26 +1,33 @@
+### Called Packages ###
import argparse
+
import transcript_extractor as te
import exon_length_filter as elf
import representative as rtcl
import poisson_sampling as ps
import writegtf as gt
import match_reprtranscript_expressionlevel as ma
+
+python_version = "3.7.13"
+module_list =[argparse]
+modul_name_list = ["argparse"]
+### Functions ###
def exe(input_file, csv, gtf, input_csv, transcript_nr,input_free = True):
file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, Input_free = input_free)
inter_mediate_file_directory = file_name +"_intermediate_file.txt"
print("Transcripts are filtered based on transcript score. Please wait...")
pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory)
print("Transcripts filtered\n")
- dictionary1 = elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = input_free)
- print(dictionary1)
-
- tsv_input = ma.match_reprTranscript_expressionLevel(input_csv, dictionary1, inter_mediate_file_directory)
+ dictionary1 = elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict)
+ df_repr = ma.match_reprTranscript_expressionLevel(dict_reprTrans=dictionary1, exprTrans=input_csv, intermediate_file= inter_mediate_file_directory,)
+ print("Finiding match between representative transcripts and expression level file")
print("Poisson sampling of transcripts")
- ps.transcript_sampling(transcript_nr, tsv_input, csv)
+ ps.transcript_sampling(transcript_nr, df_repr, csv)
print("output csv file ready")
print("writing output gtf file")
gt.gtf_file_writer(input_file, csv, gtf)
if __name__ == '__main__':
+ #te.version_control(module_list,modul_name_list,python_version)
parser = argparse.ArgumentParser(
description="transcript sampler",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
--
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