scout/parse/cytoband.py
def parse_cytoband(lines):
    """Parse iterable with cytoband coordinates
    
    
    Args:
        lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
    
    Returns:
        cytobands(dict): Dictionary with chromosome names as keys and 
                         interval trees as values
    """
    cytobands = {}
    for line in lines:
        line = line.rstrip()
        splitted_line = line.split('\t')
        chrom = splitted_line[0].lstrip('chr')
        start = int(splitted_line[1])
        stop = int(splitted_line[2])
        name = splitted_line[3]
        if chrom in cytobands:
            # Add interval to existing tree
            cytobands[chrom][start:stop] = name
        else:
            # Create a new interval tree
            new_tree = intervaltree.IntervalTree()
            # create the interval
            new_tree[start:stop] = name
            # Add the interval tree 
            cytobands[chrom] = new_tree
    
    return cytobands
def parse_cytoband(lines):
    """Parse iterable with cytoband coordinates
    
    
    Args:
        lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
    
    Returns:
        cytobands(dict): Dictionary with chromosome names as keys and 
                         interval trees as values
    """
    cytobands = {}
    for line in lines:
        line = line.rstrip()
        splitted_line = line.split('\t')
        chrom = splitted_line[0].lstrip('chr')
        start = int(splitted_line[1])
        stop = int(splitted_line[2])
        name = splitted_line[3]
        if chrom in cytobands:
            # Add interval to existing tree
            cytobands[chrom][start:stop] = name
        else:
            # Create a new interval tree
            new_tree = intervaltree.IntervalTree()
            # create the interval
            new_tree[start:stop] = name
            # Add the interval tree 
            cytobands[chrom] = new_tree
    
    return cytobands
Parse iterable with cytoband coordinates
    
    
    Args:
        lines(iterable): Strings on format "chr1\t2300000\t5400000\tp36.32\tgpos25"
    
    Returns:
        cytobands(dict): Dictionary with chromosome names as keys and 
                         interval trees as values