Extract transcripts and utrons from reads where XS tags are Assigned

[ns-rse]

Currently we have...

            if read1.get_tag("XS") == "Assigned":
                transcripts_read1 = tx2gene[read1.get_tag("XT")]
                utrons1 = [utron_coords[tx] for tx in transcripts_read1]
                utrons1 = sum(utrons1, [])
            else:
                utrons1 = list()

            if read2.get_tag("XS") == "Assigned":
                transcripts_read2 = tx2gene[read2.get_tag("XT")]
                utrons2 = [utron_coords[tx] for tx in transcripts_read2]
                utrons2 = sum(utrons2, [])
            else:
                utrons2 = list()

This is duplicated code, instead a function taking a read should be used.

It looks like its simply building a set since utrons_coords is initialised as a dictionary and only the
transcripts_read values are used as keys, nothing gets assigned to the value of the dictionary.

tx2gene is a dictionary of non-transcript data from the GTF file. where the key is the gene_id and the value is the
transcript_id

So this is pulling out of that dictionary transcript_id for reads that have been assigned where the tag ix XT.

These are then sum(), not clear why an empty list is passed in here?

Early skeleton, need to look at this more closely.

def extract_utrons(read: ?, tag: str = "XT") -> dict:
    """
    Extract utrons from assigned transcripts.

    Parameters
    ----------
    read : ?
        A read.
    tag : str
        Tag to extract, default is 'XT'.

    Returns
    -------
    tuple[transcript, utron]
        Description
    """
    if read.get_tag("XS") == "Assigned":
        return {}

def sum_utrons(read: ?, tag: str = "XT") -> int:
    return sum(extract_utrons(read, tag))