projects
/
htsworkflow.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Initial port to python3
[htsworkflow.git]
/
htsworkflow
/
pipelines
/
sequences.py
diff --git
a/htsworkflow/pipelines/sequences.py
b/htsworkflow/pipelines/sequences.py
index 87212dddbb0acda92894cf49fec9937b7f2d9e21..0a3c2fd61e856f04c9872600bc8f4025cc4ba6f4 100644
(file)
--- a/
htsworkflow/pipelines/sequences.py
+++ b/
htsworkflow/pipelines/sequences.py
@@
-7,7
+7,7
@@
import os
import types
import re
import sys
import types
import re
import sys
-from urlparse import urljoin, urlparse
+from url
lib.
parse import urljoin, urlparse
import RDF
from htsworkflow.util.rdfhelp import libraryOntology as libNS
import RDF
from htsworkflow.util.rdfhelp import libraryOntology as libNS
@@
-84,7
+84,7
@@
class SequenceFile(object):
return (self.flowcell, self.lane, self.read, self.project, self.split)
def __unicode__(self):
return (self.flowcell, self.lane, self.read, self.project, self.split)
def __unicode__(self):
- return
unicode
(self.path)
+ return
str
(self.path)
def __eq__(self, other):
"""
def __eq__(self, other):
"""
@@
-109,7
+109,7
@@
class SequenceFile(object):
return not self == other
def __repr__(self):
return not self == other
def __repr__(self):
- return
u
"<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
+ return "<%s %s %s %s>" % (self.filetype, self.flowcell, self.lane, self.path)
def make_target_name(self, root):
"""
def make_target_name(self, root):
"""
@@
-206,8
+206,8
@@
class SequenceFile(object):
def get_one(s, p):
values = get(s, p)
if len(values) > 1:
def get_one(s, p):
values = get(s, p)
if len(values) > 1:
- errmsg =
u
"To many values for %s %s"
- raise ValueError(errmsg % (
unicode(s), unicode
(p)))
+ errmsg = "To many values for %s %s"
+ raise ValueError(errmsg % (
str(s), str
(p)))
elif len(values) == 1:
return values[0]
else:
elif len(values) == 1:
return values[0]
else:
@@
-219,7
+219,7
@@
class SequenceFile(object):
rdfNS['type'],
libNS['IlluminaResult'])
if not model.contains_statement(result_statement):
rdfNS['type'],
libNS['IlluminaResult'])
if not model.contains_statement(result_statement):
- raise KeyError(
u"%s not found" % (unicode
(seq_id),))
+ raise KeyError(
"%s not found" % (str
(seq_id),))
seq_type_node = model.get_target(seq_id, libNS['file_type'])
seq_type = stripNamespace(libNS, seq_type_node)
seq_type_node = model.get_target(seq_id, libNS['file_type'])
seq_type = stripNamespace(libNS, seq_type_node)
@@
-376,7
+376,7
@@
def scan_for_sequences(dirs):
Scan through a list of directories for sequence like files
"""
sequences = []
Scan through a list of directories for sequence like files
"""
sequences = []
- if type(dirs) in
types.StringTypes
:
+ if type(dirs) in
str
:
raise ValueError("You probably want a list or set, not a string")
for d in dirs:
raise ValueError("You probably want a list or set, not a string")
for d in dirs: