diff --git a/scripts/new_exe.py b/scripts/new_exe.py index c0742721527d8c5705b2e1d6308aee732df577b7..13e5e8f1700905b2461ab8e188443a53dfaf8c23 100644 --- a/scripts/new_exe.py +++ b/scripts/new_exe.py @@ -5,28 +5,19 @@ 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): 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 = input_free) -​ 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",