def detect_one_run(run, args):
infile = os.path.join(args.indir, run)
print "processing GC-MS file:", infile
# sys.stdout("processing GCSM run:", run)
# load the input GC-MS file
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim(args.trimstart + "m", args.trimend + "m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
im = build_intensity_matrix_i(data)
# would be nice to do noise_mult*noise_level using the noise level AFTER smoothing,
# but i can't seem to get the TIC for the smoothed IM.
peak_list = call_peaks(im, tic, True, args)
return peak_list, run
def detect_one_run(run, args):
infile = os.path.join(args.indir, run)
print "processing GC-MS file:", infile
# sys.stdout("processing GCSM run:", run)
# load the input GC-MS file
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim(args.trimstart+"m",args.trimend+"m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
im = build_intensity_matrix_i(data)
# would be nice to do noise_mult*noise_level using the noise level AFTER smoothing,
# but i can't seem to get the TIC for the smoothed IM.
peak_list = call_peaks(im, tic, True, args)
return peak_list, run
def load_run(infile):
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim("4.0m", "20.0m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
return build_intensity_matrix_i(data), tic
def load_run(infile):
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim("4.0m", "20.0m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
return build_intensity_matrix_i(data), tic
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
from pyms.GCMS.Function import build_intensity_matrix_i
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
from pyms.Display.Class import Display
from pyms.Peak.Function import peak_sum_area
from pyms.Peak.IO import store_peaks
from pyms.Deconvolution.BillerBiemann.Function import BillerBiemann, \
rel_threshold, num_ions_threshold
from pyms.Simulator.Function import gcms_sim, add_gaussc_noise
# read in raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim(4101, 4350)
# Build Intensity Matrix
real_im = build_intensity_matrix_i(data)
n_scan, n_mz = real_im.get_size()
# perform necessary pre filtering
for ii in range(n_mz):
ic = real_im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
real_im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
peak_list = BillerBiemann(real_im, points=3, scans=2)
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
from pyms.GCMS.Function import build_intensity_matrix_i
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
from pyms.Display.Class import Display
from pyms.Peak.Function import peak_sum_area
from pyms.Peak.IO import store_peaks
from pyms.Deconvolution.BillerBiemann.Function import BillerBiemann, rel_threshold, num_ions_threshold
from pyms.Simulator.Function import gcms_sim, add_gaussv_noise
# read in raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim(4101, 4350)
# Build Intensity Matrix
real_im = build_intensity_matrix_i(data)
n_scan, n_mz = real_im.get_size()
# perform necessary pre filtering
for ii in range(n_mz):
ic = real_im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
real_im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
"""proc.py
"""
import sys
sys.path.append("/x/PyMS")
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
# read the raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
# info about raw data
data.info()
# trim data between scans 1000 and 2000
data.trim(1000, 2000)
# info about trimmed raw data
data.info()
# reload
data = ANDI_reader(andi_file)
# trim data between retention times, 6.5 minutes to 21 minutes
data.trim("6.5m", "21m")
# info about trimmed raw data
data.info()
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
from pyms.Peak.Class import Peak
from pyms.Display.Class import Display
from pyms.Deconvolution.BillerBiemann.Function import BillerBiemann, \
rel_threshold, num_ions_threshold
# read in raw data
andi_file = "/home/projects/PyMS_Projects/Metabolomic.Data/2010.01.28_DPI_dairy_waste_water/In/In_061108_Spring_1.CDF"
data = ANDI_reader(andi_file)
data.trim(6m, 21m)
# Build Intensity Matrix
im = build_intensity_matrix_i(data)
n_scan, n_mz = im.get_size()
# perform necessary pre filtering
for ii in range(n_mz):
ic = im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
im.set_ic_at_index(ii, ic_bc)
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
from pyms.GCMS.Function import build_intensity_matrix_i
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
from pyms.Peak.IO import store_peaks
from pyms.Deconvolution.BillerBiemann.Function import BillerBiemann, \
rel_threshold, num_ions_threshold
# read in raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim("500s", "2000s")
# Build Intensity Matrix
im = build_intensity_matrix_i(data)
n_scan, n_mz = im.get_size()
# perform necessary pre filtering
for ii in range(n_mz):
ic = im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
peak_list = BillerBiemann(im, points=9, scans=2)
print "Number of peaks found: ", len(peak_list)
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
from pyms.Peak.IO import store_peaks
from pyms.Deconvolution.BillerBiemann.Function import BillerBiemann, \
rel_threshold, num_ions_threshold
# read in raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim("500s", "2000s")
# Build Intensity Matrix
im = build_intensity_matrix_i(data)
n_scan, n_mz = im.get_size()
# perform necessary pre filtering
for ii in range(n_mz):
ic = im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
peak_list = BillerBiemann(im, points=9, scans=2)