Commit 3332032b by Eric Coissac

remove .c file generated by cython from the archive

parent ad043d25
......@@ -3,7 +3,7 @@ Created on 9 juin 2012
@author: coissac
'''
from esmre import Index
from esm import Index
from obitools.format.options import addInOutputOption, sequenceWriterGenerator,\
autoEntriesIterator
from obitools.options import getOptionManager
......
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......@@ -66,7 +66,7 @@ cpdef tuple parseFastaDescription(bytes ds, object tagparser):
return definition,info
cdef bytes _fastTagParser=b'^[a-zA-Z][a-zA-Z0-9_]* *= *[^;]*;( +[a-zA-Z][a-zA-Z0-9_]* *= *[^;]*;)*'
cdef bytes _fastTagParser=b'^[a-zA-Z][a-zA-Z.0-9_]* *= *[^;]*;( +[a-zA-Z][a-zA-Z.0-9_]* *= *[^;]*;)*'
cdef object _cfastTagParser=re.compile(_fastTagParser)
#cdef regex_t cfastTagParser
......@@ -260,7 +260,7 @@ def rawFastaIterator(file,bioseqfactory=None,
joinseq=None):
rawparser=tagparser
allparser = tagparser % '[a-zA-Z][a-zA-Z0-9_]*'
allparser = tagparser % '[a-zA-Z][a-zA-Z.0-9_]*'
tagparser = re.compile('( *%s)+' % allparser)
for entry in rawFastaEntryIterator(file):
......
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......@@ -241,7 +241,7 @@ cdef class fastqParserGenetator:
self.bioseqfactory = bioseqfactory
self.rawparser=tagparser
allparser = tagparser % '[a-zA-Z][a-zA-Z0-9_]*'
allparser = tagparser % '[a-zA-Z][a-zA-Z.0-9_]*'
tagparser = re.compile('( *%s)+' % allparser)
self.tagparser = tagparser
......
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......@@ -504,16 +504,29 @@ class Graph(object):
def __iter__(self):
return self.nodeIterator()
def __str__(self):
def dot(self,nodePredicat=None,edgePredicat=None):
def combinedPredicat(edge):
graph = edge.graph
n1 = graph.getNode(edge.node1)
n2 = graph.getNode(edge.node2)
return nodePredicat(n1) and nodePredicat(n2) and edgePredicat(edge)
if edgePredicat is not None and nodePredicat is not None:
edgePredicat = combinedPredicat
if self._directed:
kw ='digraph'
else:
kw='graph'
nodes = "\n ".join([str(x) for x in self])
edges = "\n ".join([str(x) for x in self.edgeIterator()])
nodes = "\n ".join([str(x) for x in self.nodeIterator(nodePredicat)])
edges = "\n ".join([str(x) for x in self.edgeIterator(edgePredicat)])
return "%s %s {\n %s\n\n %s\n}" % (kw,self._label,nodes,edges)
def __str__(self):
return self.dot()
class Node(object):
"""
......
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