diff --git a/scripts/new_exe.py b/scripts/new_exe.py index aaf61af68a8e200be31b6d534cd4256df4874e8d..70205475c5dcb7680391bb8d81772a9cbe4770ab 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