def get_transcripts(transcript_file):
    """
    Parses FusionInspector transcript file and returns dictionary of sequences

    :param str transcript_file: path to transcript FASTA
    :return: de novo assembled transcripts
    :rtype: dict
    """
    with open(transcript_file, 'r') as fa:
        transcripts = {}
        regex_s = r"(?P<ID>TRINITY.*)\s(?P<fusion>.*--.*):(?P<left_start>\d+)-(?P<right_start>\d+)"
        regex = re.compile(regex_s)
        while True:
            # Usually the transcript is on one line
            try:
                info = fa.next()
                seq = fa.next()

                assert info.startswith('>')

                m = regex.search(info)
                if m:
                    transcripts[m.group('ID')] = seq.strip()

            except StopIteration:
                break

            except AssertionError:
                print("WARNING: Malformed fusion transcript file")
    return transcripts
def get_transcripts ( transcript_file ) : with open ( transcript_file , 'r' ) as fa : transcripts = { } regex_s = r"(?P<ID>TRINITY.*)\s(?P<fusion>.*--.*):(?P<left_start>\d+)-(?P<right_start>\d+)" regex = re . compile ( regex_s ) while True : try : info = fa . next ( ) seq = fa . next ( ) assert info . startswith ( '>' ) m = regex . search ( info ) if m : transcripts [ m . group ( 'ID' ) ] = seq . strip ( ) except StopIteration : break except AssertionError : print ( "WARNING: Malformed fusion transcript file" ) return transcripts
Parses FusionInspector transcript file and returns dictionary of sequences

    :param str transcript_file: path to transcript FASTA
    :return: de novo assembled transcripts
    :rtype: dict