Esempi in Python per ANDI_reader.trim

Esempio n. 1

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

Esempio n. 2

File: GCMSalign.py Progetto: dkainer/easyGC

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

Esempio n. 3

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

Esempio n. 4

File: GCMSalign.py Progetto: dkainer/easyGC

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

Esempio n. 5

File: proc.py Progetto: jontay81/pyms-test

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)

Esempio n. 6

File: proc.py Progetto: ma-bio21/pyms-test

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

Esempio n. 7

"""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()

Esempio n. 8

File: proc-one-file-display.py Progetto: beyondcpu/ma-bioinformatics

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)
    

Esempio n. 9

File: proc_save_peaks.py Progetto: jontay81/pyms-test

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)

Esempio n. 10

File: proc_save_peaks.py Progetto: ma-bio21/pyms-test

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)