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import sys
sys.path.insert(0,'/global/project/projectdirs/metatlas/anaconda/lib/python2.7/site-packages' )

from metatlas import xcms
import os
# myPath = '/project/projectdirs/metatlas/original_data/kblouie/Nyogi_PSII_prelim/'
# myPath = '/project/projectdirs/metatlas/original_data/sjenkins/ENIGMA Big EMAc 1/'
myPath = '/project/projectdirs/metatlas/original_data/tls/150922_biocrust_porewater/'
myFileList = []
%system ls $myPath


    

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for file in os.listdir(myPath):
    if file.endswith(".mzML"):
#         if 'Pos' in file:
#             if '_RP' in file:
                myFileList.append('%s%s'%(myPath,file))
for f in myFileList:
    print f
xset = xcms.get_xmcs_set(myFileList)
xset = xcms.group(xset)
df = xcms.peak_table(xset)
df.head()


    

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df.to_csv('/global/homes/b/bpb/Tami_PoreWater_Neg_XCMS.xls')


    

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