[Debian-med-packaging] Bug#1085542: discosnp: Python SyntaxWarning

[Graham Inggs]

Source: discosnp
Version: 1:2.6.2-3
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/d/discosnp.html


  Setting up python3 (3.12.4-1) ...
  /usr/share/discosnp/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py:146:
SyntaxWarning: invalid escape sequence '\w'
    tig_type = len(re.findall("left_\w+_length",line))
  /usr/share/discosnp/scripts/ClassVCF_creator.py:82: SyntaxWarning:
invalid escape sequence '\d'
    parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode)
#ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
  /usr/share/discosnp/scripts/ClassVCF_creator.py:566: SyntaxWarning:
invalid escape sequence '\d'
    parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode)
#ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
  /usr/share/discosnp/scripts/ClassVCF_creator.py:639: SyntaxWarning:
invalid escape sequence '\d'
    parsingPosMut=re.findall('(\d+|[A-Za-z]|\^)',posMut)
  /usr/share/discosnp/scripts/create_filtered_vcf.py:90:
SyntaxWarning: invalid escape sequence '\w'
    tig_type = len(re.findall("left_\w+_length",line))
  /usr/share/discosnp/scripts/vcf_formatting_functions.py:94:
SyntaxWarning: invalid escape sequence '\w'
    ty = re.findall("(\w+)_higher_path",path_name)[0]
  /usr/share/discosnp/scripts/vcf_formatting_functions.py:102:
SyntaxWarning: invalid escape sequence '\d'
    unitig_len = re.findall("_unitig_length_(\d+)","|".join(splitted_1[4:6]))
  /usr/share/discosnp/scripts/vcf_formatting_functions.py:106:
SyntaxWarning: invalid escape sequence '\d'
    contig_len = re.findall("_contig_length_(\d+)","|".join(splitted_1[6:8]))
  /usr/share/discosnp/scripts/vcf_formatting_functions.py:139:
SyntaxWarning: invalid escape sequence '\d'
    POS, REF, ALT = re.findall("P_\d+:(\d+)_(\w)/(\w)",pol)[0]
  /usr/share/discosnp/scripts/vcf_formatting_functions.py:142:
SyntaxWarning: invalid escape sequence '\d'
    POS, indel_size = re.findall("P_\d+:(\d+)_(\d+)",pol)[0]
  Setting up discosnp (1:2.6.2-3+b1) ...