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
def parse_cytoband ( lines ) : 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
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