def calc_phredperbase_boxplot(infiles = None, filepattern = '', data_inpath = '',
saveprefix = '', png_filename=''):
''' Find the median, upper and lower quartile for the Phred score per base
Returns the stats and the counter dictionary.
Counter dictionary may become standard way to store mass Phred/seq bases data. '''
from collections import Counter
RecCycler = SeqRecCycler(infiles = infiles, filepattern = filepattern, data_inpath = data_inpath)
print '\nCalculating Box plot stats of phred scores per base position.\n'
# Define vars and outputs
numfiles = RecCycler.numfiles
toc = time.time()
cum_t = 0
counter_list = [0] * 101
for i in range(len(counter_list)):
counter_list[i] = Counter()
for seqrecgen in RecCycler.seqfilegen:
filename = RecCycler.curfilename
filenum = RecCycler.curfilenum
for rec in seqrecgen:
for basenum, phred in enumerate(rec.letter_annotations['phred_quality']):
counter_list[basenum][phred] += 1
loop_t = time.time() - toc - cum_t
cum_t += loop_t
print 'Finished {0} \nfile {1} of {2} after {3}'.format(filename, filenum, numfiles, time.strftime('%H:%M:%S', time.gmtime(loop_t)))
# Calculate min, max Q1, Q2, Median and Average
stats = getStatsFT(counter_list)
total_t = time.time() - toc
print 'Processed all files in {0}'.format(time.strftime('%H:%M:%S', time.gmtime(total_t)))
pklfilename = data_inpath.split('/')[-1]
pklsave(counter_list, '_'.join([pklfilename, saveprefix , 'phredCount']))
np.save( '_'.join([pklfilename, saveprefix , 'phredStats.npy']) , stats)
plotFTstats(stats, png_filename)
return stats, counter_list
total_t = time.time() - toc
print 'Finished in {0}'.format(
time.strftime('%H:%M:%S', time.gmtime(total_t)))
return TagCounter
if __name__ == '__main__':
#===========================================================================
''' RUNS SCRIPT FOR ALLL READS IN LANE 6 '''
#===========================================================================
LANE = '6'
# Set paths and file patterns
data_inpath = '/space/musselle/datasets/gazellesAndZebras/lane' + LANE + '/L6_phredprop_filtered/'
# data_inpath = '/home/musselle/data/lane' + LANE
os.chdir(data_inpath)
raw_files = glob.glob('*[0-9]-pass.fastq.bgzf')
raw_files.sort()
TagsCounter = tags_counter(infiles = raw_files, sl=(6,12))
pklsave(TagsCounter, 'L{0}_TagsCount-pass'.format(LANE))