From 13c2c54f5150a70e7b2d72c90346dd140474b860 Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Fri, 2 Dec 2022 11:12:50 +0100
Subject: [PATCH] updated exe script
---
scripts/new_exe.py | 25 ++++++++++++-------------
1 file changed, 12 insertions(+), 13 deletions(-)
diff --git a/scripts/new_exe.py b/scripts/new_exe.py
index e2bdb31..c074272 100644
--- a/scripts/new_exe.py
+++ b/scripts/new_exe.py
@@ -5,19 +5,18 @@ import representative as rtcl
import poisson_sampling as ps
import writegtf as gt
import match_reprtranscript_expressionlevel as ma
-
-
-def exe(input_file, csv, gtf, transcript_nr):
- file_name,source_pathway_name_2,deposit_pathway_name_2 = te.extract_transcript(input_file, deposit_pathway_name = True, Input_free = Input_free)
+​
+def exe(input_file, csv, gtf, 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 = input_file +"_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")
- elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = True)
-
+ elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = input_free)
+​
tsv_input = ma.output_tsv()
print("Poisson sampling of transcripts")
ps.transcript_sampling(transcript_nr, tsv_input, csv)
@@ -25,9 +24,9 @@ def exe(input_file, csv, gtf, transcript_nr):
print("writing output gtf file")
gt.gtf_file_writer(input_file, csv, gtf)
-
-
-
+​
+​
+​
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="transcript sampler",
@@ -38,4 +37,4 @@ if __name__ == '__main__':
parser.add_argument("--output_gtf", required=True, help="output gtf file")
parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample")
args = parser.parse_args()
- exe(args.annotation, args.output_csv, args.output_gtf, args.transcript_number)
\ No newline at end of file
+ exe(args.annotation, args.output_csv, args.output_gtf, args.transcript_number)
--
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