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Commit 6633ba31 authored by Laura Urbanska's avatar Laura Urbanska
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fixed invalid character error

parent 22841ac6
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...@@ -5,28 +5,19 @@ import representative as rtcl ...@@ -5,28 +5,19 @@ import representative as rtcl
import poisson_sampling as ps import poisson_sampling as ps
import writegtf as gt import writegtf as gt
import match_reprtranscript_expressionlevel as ma import match_reprtranscript_expressionlevel as ma
def exe(input_file, csv, gtf, transcript_nr,input_free = True): 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) 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 = input_file +"_intermediate_file.txt"
print("Transcripts are filtered based on transcript score. Please wait...") print("Transcripts are filtered based on transcript score. Please wait...")
pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory) pre_filter_representative_transcripts_dict = rtcl.find_repr_by_SupportLevel(inter_mediate_file_directory)
print("Transcripts filtered\n") print("Transcripts filtered\n")
elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = input_free) elf.exon_length_filter(file_name,gen_dict= pre_filter_representative_transcripts_dict, Input_free = input_free)
tsv_input = ma.output_tsv() tsv_input = ma.output_tsv()
print("Poisson sampling of transcripts") print("Poisson sampling of transcripts")
ps.transcript_sampling(transcript_nr, tsv_input, csv) ps.transcript_sampling(transcript_nr, tsv_input, csv)
print("output csv file ready") print("output csv file ready")
print("writing output gtf file") print("writing output gtf file")
gt.gtf_file_writer(input_file, csv, gtf) gt.gtf_file_writer(input_file, csv, gtf)
if __name__ == '__main__': if __name__ == '__main__':
parser = argparse.ArgumentParser( parser = argparse.ArgumentParser(
description="transcript sampler", description="transcript sampler",
......
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