[Debian-med-packaging] Bug#1085772: pbsuite: Python SyntaxWarning

[Graham Inggs]

Source: pbsuite
Version: 15.8.24+dfsg-7
User: debian-python at lists.debian.org
Usertags: syntaxwarning

Hi Maintainer

The SyntaxWarning below were emitted when this package was tested with
pipuarts[1].

Regards
Graham


[1] https://piuparts.debian.org/sid/source/p/pbsuite.html


  Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ...
  /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75:
SyntaxWarning: invalid escape sequence '\d'
    for i in re.findall("\d+|\^?[ATCGN]+", md):
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49:
SyntaxWarning: invalid escape sequence '\s'
    splRE = re.compile("\s+")
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60:
SyntaxWarning: invalid escape sequence '\s'
    splRE = re.compile("\s+")
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87:
SyntaxWarning: invalid escape sequence '\s'
    self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip())))
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475:
SyntaxWarning: invalid escape sequence '\d'
    subreadGrab = re.compile(".*/(\d+)_(\d+)$")
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499:
SyntaxWarning: invalid escape sequence '\s'
    data = re.split("\s+",line)
  /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609:
SyntaxWarning: invalid escape sequence '\s'
    data = re.split("\s+",line)
  /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110:
SyntaxWarning: invalid escape sequence '\s'
    METARE = re.compile(('##\s*(?P<key>\w+)\s*=\s*\<\s*ID\s*=\s*(?P<id>\w+)\s*'
  /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111:
SyntaxWarning: invalid escape sequence '\s'
    ',\s*(Number\s*=\s*(?P<number>[0-9.])\s*,'
  /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112:
SyntaxWarning: invalid escape sequence '\s'
    '\s*Type\s*=\s*(?P<type>\w+)\s*,)?'
  /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113:
SyntaxWarning: invalid escape sequence '\s'
    '\s*Description\s*=\s*"(?P<description>.*)"\s*\>\s*'),\
  /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22:
SyntaxWarning: invalid escape sequence '\d'
    regex = re.compile("ref\d{7}")