1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
#!/usr/bin/env python3.2
"""
Demonstration of the extraction of a specific ion chromatogram, i.e. XIC or EIC
Example:
>>> import pymzml, get_example_file
>>> example_file = get_example_file.open_example('small.pwiz.1.1.mzML')
>>> run = pymzml.run.Reader(example_file, MS1_Precision = 20e-6, MSn_Precision = 20e-6)
>>> timeDependentIntensities = []
>>> for spectrum in run:
... if spectrum['ms level'] == 1:
... matchList = spectrum.hasPeak(MASS_2_FOLLOW)
... if matchList != []:
... for mz,I in matchList:
... timeDependentIntensities.append( [ spectrum['scan time'], I , mz ])
>>> for rt, i, mz in timeDependentIntensities:
... print('{0:5.3f}\t{1:13.4f}\t{2:10}'.format( rt, i, mz ))
"""
from __future__ import print_function
import sys
import pymzml
import get_example_file
MASS_2_FOLLOW = 810.53
def main(verbose = False):
example_file = get_example_file.open_example('small.pwiz.1.1.mzML')
run = pymzml.run.Reader(example_file, MS1_Precision = 20e-6, MSn_Precision = 20e-6)
timeDependentIntensities = []
for spectrum in run:
if spectrum['ms level'] == 1:
matchList = spectrum.hasPeak(MASS_2_FOLLOW)
if matchList != []:
for mz,I in matchList:
timeDependentIntensities.append( [ spectrum['scan time'], I , mz ])
print('RT \ti \tmz')
for rt, i, mz in timeDependentIntensities:
print('{0:5.3f}\t{1:13.4f}\t{2:10}'.format( rt, i, mz ))
return
if __name__ == '__main__':
main()
|
