usage = 'usage: %prog [options] arg'

parser = OptionParser(usage)

#parser.add_option()

(options,args) = parser.parse_args()

if len(args) != 1:

parser.error('Must provide BAM file')

else:

bam_file = args[0]

align_lengths = {}

for aligned_read in pysam.Samfile(bam_file, 'rb'):

align_lengths[aligned_read.qlen] = align_lengths.get(aligned_read.qlen,0) + 1

min_len = min(align_lengths.keys())

max_len = max(align_lengths.keys())

# construct data frame

len_r = ro.IntVector(range(min_len,max_len+1))

counts_r = ro.IntVector([align_lengths.get(l,0) for l in range(min_len,max_len+1)])

df = ro.DataFrame({'length':len_r, 'counts':counts_r})

# construct full plot

gp = ggplot2.ggplot(df) + \

ggplot2.aes_string(x='length', y='counts') + \

ggplot2.geom_bar(stat='identity') + \

ggplot2.scale_x_continuous('Alignment length') + \

ggplot2.scale_y_continuous('')

# plot to file

grdevices.pdf(file='align_lengths.pdf')

gp.plot()