[med-svn] [Git][med-team/discosnp][master] 3 commits: Fix Python3.12 syntax Closes: #1085542
Andreas Tille (@tille)
gitlab at salsa.debian.org
Sat Dec 7 09:12:05 GMT 2024
Andreas Tille pushed to branch master at Debian Med / discosnp
Commits:
7663f593 by Andreas Tille at 2024-12-07T10:06:09+01:00
Fix Python3.12 syntax Closes: #1085542
- - - - -
40183e74 by Andreas Tille at 2024-12-07T10:06:44+01:00
Standards-Version: 4.7.0 (routine-update)
- - - - -
869c2e20 by Andreas Tille at 2024-12-07T10:08:21+01:00
routine-update: Ready to upload to unstable
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/python3.12-syntax.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+discosnp (1:2.6.2-4) unstable; urgency=medium
+
+ * Fix Python3.12 syntax
+ Closes: #1085542
+ * Standards-Version: 4.7.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Sat, 07 Dec 2024 10:07:19 +0100
+
discosnp (1:2.6.2-3) unstable; urgency=medium
* Add loong64 support
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
libboost-dev,
libhdf5-dev,
zlib1g-dev
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/discosnp
Vcs-Git: https://salsa.debian.org/med-team/discosnp.git
Homepage: http://colibread.inria.fr/discosnp/
=====================================
debian/patches/python3.12-syntax.patch
=====================================
@@ -0,0 +1,94 @@
+Description: Fix Python3.12 string syntax
+Bug-Debian: https://bugs.debian.org/1085542
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2024-06-07
+
+--- a/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py
++++ b/discoSnpRAD/clustering_scripts/fasta_and_cluster_to_filtered_vcf.py
+@@ -143,7 +143,7 @@ def main():
+ splitted_1 = line.split("|")
+
+ #nb_samples:
+- tig_type = len(re.findall("left_\w+_length",line))
++ tig_type = len(re.findall(r"left_\w+_length",line))
+ nb_fixed_fields = 4 + 2*tig_type
+ nb_samples = (len(splitted_1) - (nb_fixed_fields + 1))/3
+ if nb_samples % 1 != 0:
+--- a/scripts/ClassVCF_creator.py
++++ b/scripts/ClassVCF_creator.py
+@@ -79,7 +79,7 @@ def ReverseComplement(seq: str) -> str:
+
+ def shift_from_cigar_code(cigarcode, pospol):
+ # print ("shift",cigarcode,pospol)
+- parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
++ parsingCigarCode=re.findall(r'(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
+ # print (parsingCigarCode)
+ shift=0
+ pos=0
+@@ -563,7 +563,7 @@ class PATH():
+ def CigarcodeChecker(self):
+ """Checks in the cigarcode of the samfile if there is a shift in the alignment between the path and the reference"""
+ cigarcode = self.listSam[5]
+- parsingCigarCode=re.findall('(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
++ parsingCigarCode=re.findall(r'(\d+|[A-Za-z])',cigarcode) #ParsingCigarCode=['2', 'S', '3', 'M', '1', 'I', '25', 'M']
+ listPosRef=[]
+ listShift=[]
+ somme=0
+@@ -636,7 +636,7 @@ class PATH():
+ return()
+ nucleoRef=None
+ matchInt=None
+- parsingPosMut=re.findall('(\d+|[A-Za-z]|\^)',posMut)
++ parsingPosMut=re.findall(r'(\d+|[A-Za-z]|\^)',posMut)
+ while i<len(parsingPosMut):#Converts the number into integer
+ matchInt=re.match(r'\d+',parsingPosMut[i]) #Integer motif
+ if matchInt:
+--- a/scripts/create_filtered_vcf.py
++++ b/scripts/create_filtered_vcf.py
+@@ -87,7 +87,7 @@ def main():
+ if re.match(">cluster_",splitted_1[0]):
+ with_cluster = True
+ #nb_samples:
+- tig_type = len(re.findall("left_\w+_length",line))
++ tig_type = len(re.findall(r"left_\w+_length",line))
+ nb_fixed_fields = 4 + 2*tig_type
+ nb_samples = (len(splitted_1) - (nb_fixed_fields + 1))/3
+ if nb_samples % 1 != 0:
+--- a/scripts/vcf_formatting_functions.py
++++ b/scripts/vcf_formatting_functions.py
+@@ -91,7 +91,7 @@ def format_vcf(splitted_1, splitted_2, n
+ path_name = splitted_1[0].lstrip(">")
+ CHROM = path_name
+ id = path_name.split("_")[3]
+- ty = re.findall("(\w+)_higher_path",path_name)[0]
++ ty = re.findall(r"(\w+)_higher_path",path_name)[0]
+
+ if ty != "SNP":
+ ty = "INS"
+@@ -99,11 +99,11 @@ def format_vcf(splitted_1, splitted_2, n
+ INFO = f"Ty={ty};Rk={rank};"
+ position_offset = 0
+ if tig_type >0:
+- unitig_len = re.findall("_unitig_length_(\d+)","|".join(splitted_1[4:6]))
++ unitig_len = re.findall(r"_unitig_length_(\d+)","|".join(splitted_1[4:6]))
+ position_offset = int(unitig_len[0])
+ INFO += f"UL={unitig_len[0]};UR={unitig_len[1]};";
+ if tig_type == 2:
+- contig_len = re.findall("_contig_length_(\d+)","|".join(splitted_1[6:8]))
++ contig_len = re.findall(r"_contig_length_(\d+)","|".join(splitted_1[6:8]))
+ position_offset = int(contig_len[0]) # if contig POS = POS + left_contig_len
+ INFO += f"CL={contig_len[0]};CR={contig_len[1]};"
+ else:
+@@ -136,10 +136,10 @@ def format_vcf(splitted_1, splitted_2, n
+ i = 1
+ for pol in cigar:
+ if ty == "SNP":
+- POS, REF, ALT = re.findall("P_\d+:(\d+)_(\w)/(\w)",pol)[0]
++ POS, REF, ALT = re.findall(r"P_\d+:(\d+)_(\w)/(\w)",pol)[0]
+ POS = int(POS) + position_offset # POS is 1-based
+ else: # INDEL
+- POS, indel_size = re.findall("P_\d+:(\d+)_(\d+)",pol)[0]
++ POS, indel_size = re.findall(r"P_\d+:(\d+)_(\d+)",pol)[0]
+ POS = int(POS) + position_offset # 1-based
+ ALT = sequence[(POS-1):(POS+int(indel_size))]
+ REF = ALT[0]
=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ spelling.patch
adapt_test_scripts.patch
2to3.patch
shell_syntax.patch
+python3.12-syntax.patch
View it on GitLab: https://salsa.debian.org/med-team/discosnp/-/compare/21d3f942c48f43581b8b9abc1497b43c0d3091d7...869c2e20a1fbd1477e471c4c05305d6290f24ddc
--
View it on GitLab: https://salsa.debian.org/med-team/discosnp/-/compare/21d3f942c48f43581b8b9abc1497b43c0d3091d7...869c2e20a1fbd1477e471c4c05305d6290f24ddc
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20241207/3cba3c92/attachment-0001.htm>
More information about the debian-med-commit
mailing list