# 3.7. Regex patterns

This file hosts a centralized point for all regex patterns used in pymzML

Note

We need some comment lines for each regex, i.e. what does it catch .. maybe with examples and stuff …

Collection of regular expressions to catch spectrum XML-tags.

`pymzml.regex_patterns.``CHROMATOGRAM_AND_SPECTRUM_PATTERN_WITH_ID` = re.compile('<\\s*(chromatogram|spectrum)\\s*(id=(\\".*?\\")|index=\\".*?\\")\\s(id=(\\".*?\\"))*\\s*.*\\sdefaultArrayLength=\\"[0-9]+\\">')

  Regex to catch combined chromatogram and spectrum patterns

`pymzml.regex_patterns.``CHROMATOGRAM_CLOSE_PATTERN` = re.compile(b'</chromatogram>')

  Regex to catch spectrum xml close tags

`pymzml.regex_patterns.``CHROMATOGRAM_ID_PATTERN` = re.compile('<chromatogram.*id="(.*?)".*?>')

  Regex to catch chromatogram id patterns

`pymzml.regex_patterns.``CHROMATOGRAM_PATTERN` = re.compile('<chromatogram.*id="(.*?)".*?>')

  Regex to catch chromatogram id pattern (again ?)

`pymzml.regex_patterns.``FILE_ENCODING_PATTERN` = re.compile(b'encoding="(?P<encoding>[A-Za-z0-9-]*)"')

  Regex to catch xml file encoding

`pymzml.regex_patterns.``MOBY_DICK_CHAPTER_PATTERN` = re.compile('CHAPTER ([0-9]+).*')

  Regex to catch moby dick chapter number used in the index gezip writer example.

`pymzml.regex_patterns.``SIM_INDEX_PATTERN` = re.compile(b'(?P<type>idRef=")(?P<nativeID>.*)">(?P<offset>[0-9]*)</offset>')

  Regex pattern for SIM index

`pymzml.regex_patterns.``SPECTRUM_CLOSE_PATTERN` = re.compile(b'</spectrum>')

  Regex to catch spectrum xml close tags

`pymzml.regex_patterns.``SPECTRUM_ID_PATTERN2` = re.compile('(scan|scanId)=(\\d+)')

  Simplified spectrum id regex. Greedly catches ints at the end of line

`pymzml.regex_patterns.``SPECTRUM_INDEX_PATTERN` = re.compile(b'(?P<type>(scan=|nativeID="))(?P<nativeID>[0-9]*)">"(?P<offset>[0-9]*)</offset>')

  Regex pattern for spectrum index works for obo format 1.1.0 until <last version checked>

  Catches:

    1. demo 1

    2. demo 2

`pymzml.regex_patterns.``SPECTRUM_OPEN_PATTERN` = re.compile(b'<*spectrum[^>]*index="(?P<index>[0-9]+)" id="(?P<id>[^"]+)" defaultArrayLength="[0-9]+">')

  Regex to catch specturm open xml tag with encoded array length

`pymzml.regex_patterns.``SPECTRUM_TAG_PATTERN` = re.compile('<spectrum.*?id="(?P<index>[^"]+)".*?>')

  Regex to catch spectrum tag pattern