def expr_list(pyms_datadir):
with tempfile.TemporaryDirectory() as tmpdir:
outputdir = pathlib.Path(tmpdir)
# Create experiment files
for jcamp_file in eley_codes:
im = build_intensity_matrix_i(
JCAMP_reader(pyms_datadir / f"{jcamp_file}.JDX"))
# Intensity matrix size (scans, masses)
n_scan, n_mz = im.size
# noise filter and baseline correct
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)
peak_list = BillerBiemann(im, points=9, scans=2)
print('#')
apl = rel_threshold(peak_list, 2)
new_peak_list = num_ions_threshold(apl, 3, 3000)
print('#')
# ignore TMS ions and set mass range
for peak in new_peak_list:
peak.crop_mass(50, 400)
peak.null_mass(73)
peak.null_mass(147)
# find area
area = peak_sum_area(im, peak)
peak.area = area
area_dict = peak_top_ion_areas(im, peak)
peak.ion_areas = area_dict
expr = Experiment(jcamp_file, new_peak_list)
# set time range for all experiments
expr.sele_rt_range(["6.5m", "21m"])
print('#')
expr.dump(outputdir / f"{jcamp_file}.expr")
print('#')
# Load experiments
expr_list = []
for expr_code in eley_codes:
expr = load_expr(outputdir / f"{expr_code}.expr")
assert isinstance(expr, Experiment)
expr_list.append(expr)
yield expr_list
for peak in peak_list:
peak.crop_mass(51, 540)
peak.null_mass(73)
peak.null_mass(147)
area = peak_sum_area(im, peak)
peak.area = area
# Create an |Experiment|.
# In[8]:
from pyms.Experiment import Experiment
expr = Experiment("a0806_077", peak_list)
# Set the time range for all Experiments
# In[9]:
expr.sele_rt_range(["6.5m", "21m"])
# Save the experiment to disk.
# In[10]:
expr.dump(output_directory / "experiments" / "a0806_077.expr")
#
# ignore TMS ions and use same mass range for all experiments
for peak in peak_list:
peak.crop_mass(50, 540)
peak.null_mass(73)
peak.null_mass(147)
# find peak areas
area = peak_sum_area(im, peak)
peak.area = area
area_dict = peak_top_ion_areas(im, peak)
peak.ion_areas = area_dict
# create an experiment
expr = Experiment(expr_code, peak_list)
# use same retention time range for all experiments
lo_rt_limit = "6.5m"
hi_rt_limit = "21m"
print(
f"\t -> Selecting retention time range between '{lo_rt_limit}' and '{hi_rt_limit}'"
)
expr.sele_rt_range([lo_rt_limit, hi_rt_limit])
# store processed data as experiment object
output_file = "output/" + expr_code + ".expr"
print(f"\t -> Saving the result as '{output_file}'")
expr.dump(output_file)
