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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
|
"""Collection of regular expressions to catch spectrum XML-tags."""
import re
import regex
SPECTRUM_INDEX_PATTERN = re.compile(
b'(?P<type>(scan=|nativeID="))(?P<nativeID>[0-9]*)">"'
b"(?P<offset>[0-9]*)</offset>"
)
"""
Regex pattern for spectrum index
works for obo format 1.1.0 until <last version checked>
Catches:
#. demo 1
#. demo 2
"""
SIM_INDEX_PATTERN = re.compile(
b'(?P<type>idRef=")(?P<nativeID>.*)">(?P<offset>[0-9]*)</offset>'
)
"""
Regex pattern for SIM index
"""
SPECTRUM_PATTERN3 = regex.compile(r"((\w+)=(\w+\s*))+")
SPECTRUM_ID_PATTERN = re.compile(r'="{0,1}([0-9]*)"{0,1}>{0,1}$')
SPECTRUM_ID_PATTERN2 = re.compile(r'(scan|scanId)=(\d+)')
"""
Simplified spectrum id regex. Greedly catches ints at the end of line
"""
FILE_ENCODING_PATTERN = re.compile(b'encoding="(?P<encoding>[A-Za-z0-9-]*)"')
"""
Regex to catch xml file encoding
"""
MOBY_DICK_CHAPTER_PATTERN = re.compile(r"CHAPTER ([0-9]+).*")
"""
Regex to catch moby dick chapter number used in the index gezip writer example.
"""
SPECTRUM_OPEN_PATTERN = re.compile(b'<*spectrum[^>]*(index|id)="(.*?)".*(index|id)="(.*?)"')
"""
Regex to catch specturm open xml tag with encoded array length
"""
SPECTRUM_OPEN_PATTERN_SIMPLE = re.compile(rb"<spectrum ")
SPECTRUM_ID_PATTERN_SIMPLE = re.compile(rb"<*spectrum[^>]*id=\"(?P<id>[^\"]+)\"")
SPECTRUM_DEFAULTARRY_PATTERN_SIMPLE = re.compile(rb"<*spectrum[^>]*defaultArrayLength=\"[0-9]+\">")
CHROMO_OPEN_PATTERN = re.compile(b'<chromatogram\\s.*?id="(.*?)"')
SPECTRUM_CLOSE_PATTERN = re.compile(b"</spectrum>")
"""Regex to catch spectrum xml close tags"""
CHROMATOGRAM_CLOSE_PATTERN = re.compile(b"</chromatogram>")
"""Regex to catch spectrum xml close tags"""
SPECTRUM_TAG_PATTERN = re.compile(r'<spectrum.*?id="(?P<index>[^"]+)".*?>')
"""Regex to catch spectrum tag pattern"""
CHROMATOGRAM_ID_PATTERN = re.compile(r'<chromatogram.*id="(.*?)".*?>')
"""Regex to catch chromatogram id patterns"""
CHROMATOGRAM_PATTERN = re.compile(r'<chromatogram.*id="(.*?)".*?>')
"""Regex to catch chromatogram id pattern (again ?)"""
CHROMATOGRAM_AND_SPECTRUM_PATTERN_WITH_ID = re.compile(
r"<\s*(chromatogram|spectrum)\s*(id=(\".*?\")|index=\".*?\")\s(id=(\".*?\"))*\s*.*\sdefaultArrayLength=\"[0-9]+\">"
)
"""Regex to catch combined chromatogram and spectrum patterns"""
INDEX_LIST_OFFSET_PATTERN = re.compile(
b"<indexListOffset>(?P<indexListOffset>[0-9]*)</indexListOffset>"
)
CHROMATOGRAM_OFFSET_PATTERN = re.compile(
b'(?P<WTF>[nativeID|idRef])="TIC">(?P<offset>[0-9]*)</offset'
)
|
