added new exe python file and modified match transcript script

scripts/match_reprtranscript_expressionlevel.py

@@ -187,14 +187,14 @@ 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_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))
+#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__":  
-    match_reprTranscript_expressionLevel()
+#if __name__ == "__main__":  
+#    match_reprTranscript_expressionLevel()
  

scripts/new_exe.py

+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
+
+
+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)
+    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)
+
+    tsv_input = ma.output_tsv()
+    print("Poisson sampling of transcripts")
+    ps.transcript_sampling(transcript_nr, tsv_input, csv)
+    print("output csv file ready")
+    
+    print("writing output gtf file")
+    gt.gtf_file_writer(input_file, csv, gtf)
+
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        description="transcript sampler",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter
+    )
+    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("--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)
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