Skip to content
Snippets Groups Projects
Commit 6633ba31 authored by Laura Urbanska's avatar Laura Urbanska
Browse files

fixed invalid character error

parent 22841ac6
No related branches found
No related tags found
No related merge requests found
......@@ -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",
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment