diff --git a/scripts/exon_length_filter.py b/scripts/exon_length_filter.py index 23806d88185e681f8945b057dd8efe1e8ba08b6d..f8b462167aea40dc2e84127b69f601b975def9bf 100644 --- a/scripts/exon_length_filter.py +++ b/scripts/exon_length_filter.py @@ -1,6 +1,6 @@ #### Exon length filter ##### """Exon length filter -Version 1.1.0""" +Version 2.0.0""" ### Called Packages ### import re import os @@ -159,11 +159,11 @@ def _exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),dep return(representative_transcript) def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),deposit_pathway_name =os.getcwd(),gen_dict = {"ENSG00000160072":["ENST00000673477","ENST00000472194","ENST00000378736","ENST00000308647","ENST00000442483"],"ENSG00000225972":["ENST00000416931"],"ENSG00000279928":["ENST00000624431","ENST00000424215"],"ENSG00000142611":["ENST00000378391","ENST00000607632","ENST00000511072"]},Input_free = False): - """This function filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene ans saves tham in a "," seperated csv file. + """This function filters a dictionary of genes and there transcripts by the length of there exons an selects the longes transcript for each gene and returns an dictionary {gene_ID : transcript_ID}. Expected inputs: file_name: str ; default = test #the name of the gft file you want to look at source_pathway_name: str ; default = current work directory #path of the gtf file - deposit_pathway_name: str ; default = current work directory #path for saving the csv file + deposit_pathway_name: str ; default = current work directory #path for files gen_dict:dict{key == gene ID:[transcript IDs that belong to that gene]} Input_free: tuple ; default = False # this input should be set to True for automation""" @@ -176,8 +176,8 @@ def exon_length_filter(file_name = "test",source_pathway_name = os.getcwd(),depo pre_existing_file = te.__searche_for_preexisting_files(search_profile,deposit_pathway_name) if pre_existing_file == False: representative_transcript = _exon_length_filter(file_name,source_pathway_name,deposit_pathway_name,gen_dict) - _representative_transcript_csv(representative_transcript,file_name,deposit_pathway_name) print("\nRepresentative transcripts collected") + return(representative_transcript) if __name__ == "__main__":