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Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git

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This commit is contained in:
Celine Mercier
2016-12-19 10:31:18 +01:00
parent 857a5198e4 fc805e5443
commit 3bf5260174
2 changed files with 13 additions and 11 deletions
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2
distutils.ext/obidistutils/core.py
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@ -40,6 +40,7 @@ def findPackage(root,base=None):
def findCython(root,base=None,pyrexs=None): def findCython(root,base=None,pyrexs=None):
setupdir = os.path.dirname(sys.argv[0]) setupdir = os.path.dirname(sys.argv[0])
csourcedir = os.path.join(setupdir,"src")
pyrexs=[] pyrexs=[]
if base is None: if base is None:
@ -53,6 +54,7 @@ def findCython(root,base=None,pyrexs=None):
[pyrex] [pyrex]
) )
) )
pyrexs[-1].include_dirs.append(csourcedir)
try: try:
cfiles = os.path.splitext(pyrex)[0]+".cfiles" cfiles = os.path.splitext(pyrex)[0]+".cfiles"
cfilesdir = os.path.dirname(cfiles) cfilesdir = os.path.dirname(cfiles)

22
python/obitools3/obidms/_obiseq.pyx
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@ -18,10 +18,10 @@ cdef class OBI_Seq(dict) :
# sequence id property getter and setter # sequence id property getter and setter
@property @property
def id(self): def id(self): # @ReservedAssignment
return self._id return self._id
@id.setter @id.setter
def id(self, str new_id): def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self._id = new_id self._id = new_id
self[bytes2str(ID_COLUMN)] = new_id self[bytes2str(ID_COLUMN)] = new_id
@ -30,7 +30,7 @@ cdef class OBI_Seq(dict) :
def seq(self): def seq(self):
return self._seq return self._seq
@seq.setter @seq.setter
def seq(self, object new_seq): def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq self._seq = new_seq
self["SEQ"] = new_seq # TODO discuss self["SEQ"] = new_seq # TODO discuss
@ -39,7 +39,7 @@ cdef class OBI_Seq(dict) :
def definition(self): def definition(self):
return self._definition return self._definition
@definition.setter @definition.setter
def definition(self, object new_definition): def definition(self, object new_definition): # @DuplicatedSignature
self._definition = new_definition self._definition = new_definition
self[bytes2str(DEFINITION_COLUMN)] = new_definition self[bytes2str(DEFINITION_COLUMN)] = new_definition
@ -51,7 +51,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
def seq(self): def seq(self):
return self._seq return self._seq
@seq.setter @seq.setter
def seq(self, object new_seq): def seq(self, object new_seq): # @DuplicatedSignature
self._seq = new_seq self._seq = new_seq
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
@ -60,7 +60,7 @@ cdef class OBI_Nuc_Seq(OBI_Seq) :
def quality(self): def quality(self):
return self._quality return self._quality
@quality.setter @quality.setter
def quality(self, object new_quality): def quality(self, object new_quality): # @DuplicatedSignature
self._quality = new_quality self._quality = new_quality
self[bytes2str(QUALITY_COLUMN)] = new_quality self[bytes2str(QUALITY_COLUMN)] = new_quality
@ -74,10 +74,10 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
# sequence id property getter and setter # sequence id property getter and setter
@property @property
def id(self): def id(self): # @ReservedAssignment @DuplicatedSignature
return self[bytes2str(ID_COLUMN)] return self[bytes2str(ID_COLUMN)]
@id.setter @id.setter
def id(self, str new_id): def id(self, str new_id): # @ReservedAssignment @DuplicatedSignature
self[bytes2str(ID_COLUMN)] = new_id self[bytes2str(ID_COLUMN)] = new_id
# sequence definition property getter and setter # sequence definition property getter and setter
@ -85,7 +85,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
def definition(self): def definition(self):
return self[bytes2str(DEFINITION_COLUMN)] return self[bytes2str(DEFINITION_COLUMN)]
@definition.setter @definition.setter
def definition(self, str new_def): def definition(self, str new_def): # @DuplicatedSignature
self[bytes2str(DEFINITION_COLUMN)] = new_def self[bytes2str(DEFINITION_COLUMN)] = new_def
# nuc_seq property getter and setter # nuc_seq property getter and setter
@ -93,7 +93,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
def nuc_seq(self): def nuc_seq(self):
return self[bytes2str(NUC_SEQUENCE_COLUMN)] return self[bytes2str(NUC_SEQUENCE_COLUMN)]
@nuc_seq.setter @nuc_seq.setter
def nuc_seq(self, object new_seq): def nuc_seq(self, object new_seq): # @DuplicatedSignature
self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq self[bytes2str(NUC_SEQUENCE_COLUMN)] = new_seq
# quality property getter and setter # quality property getter and setter
@ -101,7 +101,7 @@ cdef class OBI_Nuc_Seq_Stored(OBIView_line) :
def quality(self): def quality(self):
return self[bytes2str(QUALITY_COLUMN)] return self[bytes2str(QUALITY_COLUMN)]
@quality.setter @quality.setter
def quality(self, object new_qual): def quality(self, object new_qual): # @DuplicatedSignature
if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists if (type(new_qual) == list) or (new_qual is None) : # TODO check that quality column exists
self[bytes2str(QUALITY_COLUMN)] = new_qual self[bytes2str(QUALITY_COLUMN)] = new_qual
else : # Quality is in str form else : # Quality is in str form