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Description: Fix Python3.12 string syntax
Bug-Debian: https://bugs.debian.org/1085416
Author: Andreas Tille <tille@debian.org>
Last-Update: 2024-12-05
--- a/changeo/Applications.py
+++ b/changeo/Applications.py
@@ -280,7 +280,7 @@ def getIgBLASTVersion(exec=default_igbla
printError('Running command: %s\n%s' % (' '.join(cmd), e.output))
# Extract version number
- match = re.search('(?<=Package: igblast )(\d+\.\d+\.\d+)', stdout_str)
+ match = re.search(r'(?<=Package: igblast )(\d+\.\d+\.\d+)', stdout_str)
version = match.group(0)
- return version
\ No newline at end of file
+ return version
--- a/changeo/IO.py
+++ b/changeo/IO.py
@@ -526,8 +526,8 @@ class IMGTReader:
Returns:
dict : database entries for gene calls.
"""
- clean_regex = re.compile('(,)|(\(see comment\))')
- delim_regex = re.compile('\sor\s')
+ clean_regex = re.compile(r'(,)|(\(see comment\))')
+ delim_regex = re.compile(r'\sor\s')
# Gene calls
v_str = summary['V-GENE and allele']
@@ -953,7 +953,7 @@ class IgBLASTReader:
# Extract column names from comments
f = next((x for x in chunk if x.startswith('# V-(D)-J rearrangement summary')))
- f = re.search('summary for query sequence \((.+)\)\.', f).group(1)
+ f = re.search(r'summary for query sequence \((.+)\)\.', f).group(1)
columns = [summary_map[x.strip()] for x in f.split(',')]
# Extract first row as a list
@@ -987,7 +987,7 @@ class IgBLASTReader:
# Extract column names from comments
f = next((x for x in chunk if x.startswith('# Sub-region sequence details')))
- f = re.search('sequence details \((.+)\)', f).group(1)
+ f = re.search(r'sequence details \((.+)\)', f).group(1)
columns = [cdr3_map[x.strip()] for x in f.split(',')]
# Extract first CDR3 as a list and remove the CDR3 label
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