[med-svn] [Git][med-team/python-pyfaidx][upstream] New upstream version 0.5.9.5

[Nilesh Patra]

Nilesh Patra pushed to branch upstream at Debian Med / python-pyfaidx


Commits:
96d9c2ab by Nilesh Patra at 2021-04-21T14:11:28+05:30
New upstream version 0.5.9.5
- - - - -


2 changed files:

- pyfaidx/__init__.py
- pyfaidx/cli.py


Changes:

=====================================
pyfaidx/__init__.py
=====================================
@@ -29,7 +29,7 @@ if sys.version_info > (3, ):
 
 dna_bases = re.compile(r'([ACTGNactgnYRWSKMDVHBXyrwskmdvhbx]+)')
 
-__version__ = '0.5.9.2'
+__version__ = '0.5.9.5'
 
 
 class KeyFunctionError(ValueError):


=====================================
pyfaidx/cli.py
=====================================
@@ -126,13 +126,13 @@ def transform_sequence(args, fasta, name, start=None, end=None):
     elif args.transform == 'nucleotide':
         ss = str(s).upper()
         nucs = defaultdict(int)
-        nucs.update([(c, str(ss).count(c)) for c in set(str(ss))])
+        nucs.update([(c, ss.count(c)) for c in set(ss)])
         A = nucs.pop('A', 0)
         T = nucs.pop('T', 0)
         C = nucs.pop('C', 0)
         G = nucs.pop('G', 0)
         N = nucs.pop('N', 0)
-        others = '|'.join([':'.join((k, v)) for k, v in nucs.items()])
+        others = '|'.join([':'.join((k, str(v))) for k, v in nucs.items()])
         return '{sname}\t{sstart}\t{send}\t{A}\t{T}\t{C}\t{G}\t{N}\t{others}\n'.format(sname=s.name, sstart=s.start, send=s.end, **locals())
     elif args.transform == 'transposed':
         return '{name}\t{start}\t{end}\t{seq}\n'.format(name=s.name, start=s.start, end=s.end, seq=str(s))



View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/96d9c2abe6188a06882a6a1552f9a52b41cc2529

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View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/96d9c2abe6188a06882a6a1552f9a52b41cc2529
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