updated new exe file

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)