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Description: fix Python SyntaxWarning.
Author: Étienne Mollier <emollier@debian.org>
Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1087097
Forwarded: no
Last-Update: 2024-12-05
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
--- srst2.orig/database_clustering/VFDB_cdhit_to_csv.py
+++ srst2/database_clustering/VFDB_cdhit_to_csv.py
@@ -50,7 +50,7 @@
for record in SeqIO.parse(open(args.infile, "r"), "fasta"):
full_name = record.description
genus = full_name.split("[")[-1].split()[0]
- in_brackets = re.findall('\((.*?)\)', full_name)
+ in_brackets = re.findall(r'\((.*?)\)', full_name)
seqID = full_name.split("(")[0]
if in_brackets[0].startswith('gi:'):
gene = in_brackets[1]
--- srst2.orig/database_clustering/align_plot_tree_min3.py
+++ srst2/database_clustering/align_plot_tree_min3.py
@@ -25,7 +25,7 @@
#alignment()
-r('''
+r(r'''
require(ape, quietly=TRUE)
all_files = list.files("/home/UNIMELB/hdashnow/resistance_database/by_gene",
--- srst2.orig/scripts/getmlst.py
+++ srst2/scripts/getmlst.py
@@ -178,7 +178,7 @@
print("\n For SRST2, remember to check what separator is being used in this allele database")
head = os.popen('head -n 1 ' + species_all_fasta_filename).read().rstrip()
- m = re.match('>(.*)([_-])(\d*)',head).groups()
+ m = re.match(r'>(.*)([_-])(\d*)',head).groups()
if len(m)==3:
print()
print(" Looks like --mlst_delimiter '" + m[1] + "'")
--- srst2.orig/scripts/srst2.py
+++ srst2/scripts/srst2.py
@@ -87,7 +87,7 @@
# Mapping parameters for bowtie2
parser.add_argument('--stop_after', type=str, required=False, help='Stop mapping after this number of reads have been mapped (otherwise map all)')
- parser.add_argument('--other', type=str, help='Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False)
+ parser.add_argument('--other', type=str, help=r'Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".', required=False)
# Filtering parameters for initial SAM file
parser.add_argument('--max_unaligned_overlap', type=int, default=10, help='Read discarded from alignment if either of its ends has unaligned '+\
@@ -96,7 +96,7 @@
# Samtools parameters
parser.add_argument('--mapq', type=int, default=1, help='Samtools -q parameter (default 1)')
parser.add_argument('--baseq', type=int, default=20, help='Samtools -Q parameter (default 20)')
- parser.add_argument('--samtools_args', type=str, help='Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False)
+ parser.add_argument('--samtools_args', type=str, help=r'Other arguments to pass to samtools mpileup (must be escaped, e.g. "\-A").', required=False)
# Reporting options
parser.add_argument('--output', type=str, required=True, help='Prefix for srst2 output files')
@@ -238,7 +238,7 @@
continue
flag = int(fields[1])
flag = (flag - 256) if (flag & 256) else flag
- m = re.search("NM:i:(\d+)\s",line)
+ m = re.search(r"NM:i:(\d+)\s",line)
if m != None:
num_mismatch = m.group(1)
if int(num_mismatch) <= int(max_mismatch):
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