In [2]:

    

import sys
sys.path.append( '/Users/bpb/repos/metatlas/metatlas' )
import pymzml
import h5_query as h5q
import mzml_loader as mzml_loader
import numpy as np
import tables
import matplotlib.pyplot as plt
%matplotlib inline
%config InlineBackend.figure_format = 'svg'


    

In [3]:

    

mypath = '/Users/bpb/Downloads/Pete/'
import os
for file in os.listdir(mypath):
    if file.endswith(".mzML"):
        filename = '%s%s' % (mypath,file)
        mzml_loader.mzml_to_hdf(filename)
        print filename


    

    




/Users/bpb/Downloads/Pete/NEG_13Bmsms.mzML
/Users/bpb/Downloads/Pete/NEG_14Cmsms.mzML
/Users/bpb/Downloads/Pete/NEG_1Bmsms.mzML
/Users/bpb/Downloads/Pete/NEG_5Dmsms.mzML
/Users/bpb/Downloads/Pete/POS_13Bmsms.mzML
/Users/bpb/Downloads/Pete/POS_14Cmsms.mzML
/Users/bpb/Downloads/Pete/POS_1Bmsms.mzML
/Users/bpb/Downloads/Pete/POS_1Bmsms_re_proteo.mzML
/Users/bpb/Downloads/Pete/POS_5Dmsms.mzML

In [6]:

    

fid = tables.open_file('/Users/bpb/Downloads/Pete/POS_5Dmsms.h5',mode='r')


rt,intensities = h5q.get_chromatogram(fid,0,1000,1,1)
plt.plot(rt,intensities)
plt.show()

fid.close()