make_weblogo.py

def make_weblogo(input_seqs, title, resolution, file_format = 'png', add_n = True, labels = None):
    seqs = weblogo.seq.SeqList( alphabet = weblogo.seq.unambiguous_protein_alphabet )
    seq_len = None
    for seq in input_seqs:                                                                                                                         if seq_len == None:                                                                                                                            seq_len = len(seq)                                                                                                                     else:                                                                                                                                          assert( seq_len == len(seq) )                                                                                                          seqs.append(seq)                                                                                                                                                                                                                                                                  data = weblogo.LogoData.from_seqs(seqs)                                                                                                                                                                                                                                               options = weblogo.LogoOptions()                                                                                                            if add_n:
        options.logo_title = '%s (n=%d)' % (title, len(input_seqs))
    else:
        options.logo_title = title
    if labels != None:
        if len(labels) != seq_len:
            print( len(labels), seq_len )
        options.annotate = labels

    options.show_fineprint = False
    # options.annotate = wt_seq
    # options.unit_name = 'probability'
    options.number_fontsize = 2.4
    # options.show_yaxis = False
    options.fontsize = 2
    options.logo_margin = 5
    options.show_boxes = False
    options.stack_width = 100
    options.small_fontsize = 28
    options.fontsize = 20
    options.title_fontsize = 30
    options.number_fontsize = 21
    options.color_scheme = weblogo.std_color_schemes['chemistry']
    #options.stack_height = 200
    # options.shrink_fraction = False
    options.resolution = resolution
    if file_format == 'png':
        return weblogo.png_formatter( data, weblogo.LogoFormat(data, options) )
    elif file_format == 'svg':
        return weblogo.svg_formatter( data, weblogo.LogoFormat(data, options) )
    else:
        raise Exception('Bad file format')