From 49674fc82acf336ffd33be43d67306735cb02a54 Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Fri, 2 Dec 2022 11:53:31 +0100
Subject: [PATCH] updated new exe file
---
scripts/new_exe.py | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/scripts/new_exe.py b/scripts/new_exe.py
index 13e5e8f..aaf61af 100644
--- a/scripts/new_exe.py
+++ b/scripts/new_exe.py
@@ -5,14 +5,16 @@ 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,input_free = True):
+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 = input_file +"_intermediate_file.txt"
+ 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")
- elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = input_free)
- tsv_input = ma.output_tsv()
+ 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)
print("Poisson sampling of transcripts")
ps.transcript_sampling(transcript_nr, tsv_input, csv)
print("output csv file ready")
@@ -25,7 +27,8 @@ if __name__ == '__main__':
)
parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
parser.add_argument("--output_csv", required=True, help="output csv file")
+ parser.add_argument("--input_csv", required=True, help="output csv file")
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)
+ exe(args.annotation, args.output_csv, args.output_gtf, args.input_csv, args.transcript_number)
--
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