Figure_4/analysis_utils/parse_RNA-PET_bedtools_output.py
def make_transcript_PET_dict(infile):
    """ Given a bedtools intersect file, this function creates a dictionary
        mapping each transcript_ID to a set containing the RNA-PET IDs that
        it matched to. """

    transcript_2_pet = {}   

    with open(infile, 'r') as f:
        for line in f:
            line = line.strip()
            entry = line.split("\t")

            transcript_ID = entry[3]
            rna_pet_ID = entry[9]

            if transcript_ID in transcript_2_pet:
                transcript_2_pet[transcript_ID].add(rna_pet_ID)
            elif rna_pet_ID != "-1":
                transcript_2_pet[transcript_ID] = set()
                transcript_2_pet[transcript_ID].add(rna_pet_ID)
            else:
               transcript_2_pet[transcript_ID] = set()
            
    return transcript_2_pet
 Given a bedtools intersect file, this function creates a dictionary
        mapping each transcript_ID to a set containing the RNA-PET IDs that
        it matched to. 
Given a bedtools intersect file, this function creates a dictionary
mapping each transcript_ID to a set containing the RNA-PET IDs that
it matched to.
Given a bedtools intersect file this function creates a dictionary mapping each transcript_ID to a set containing the RNA - PET IDs that it matched to .
def make_transcript_PET_dict(infile):
    transcript_2_pet = {}   
    with open(infile, 'r') as f:
        for line in f:
            line = line.strip()
            entry = line.split("\t")
            transcript_ID = entry[3]
            rna_pet_ID = entry[9]
            if transcript_ID in transcript_2_pet:
                transcript_2_pet[transcript_ID].add(rna_pet_ID)
            elif rna_pet_ID != "-1":
                transcript_2_pet[transcript_ID] = set()
                transcript_2_pet[transcript_ID].add(rna_pet_ID)
            else:
               transcript_2_pet[transcript_ID] = set()
    return transcript_2_pet
def make_transcript_PET_dict ( infile ) : transcript_2_pet = { } with open ( infile , 'r' ) as f : for line in f : line = line . strip ( ) entry = line . split ( "\t" ) transcript_ID = entry [ 3 ] rna_pet_ID = entry [ 9 ] if transcript_ID in transcript_2_pet : transcript_2_pet [ transcript_ID ] . add ( rna_pet_ID ) elif rna_pet_ID != "-1" : transcript_2_pet [ transcript_ID ] = set ( ) transcript_2_pet [ transcript_ID ] . add ( rna_pet_ID ) else : transcript_2_pet [ transcript_ID ] = set ( ) return transcript_2_pet
Given a bedtools intersect file, this function creates a dictionary
mapping each transcript_ID to a set containing the RNA-PET IDs that
it matched to.
Given a bedtools intersect file this function creates a dictionary mapping each transcript_ID to a set containing the RNA - PET IDs that it matched to .
""" Given a bedtools intersect file, this function creates a dictionary
        mapping each transcript_ID to a set containing the RNA-PET IDs that
        it matched to. """
infile