Fixed merge conflict

python/obitools3/apps/progress.pyx

@@ -7,7 +7,9 @@ Created on 27 mars 2016
 '''
 
 import sys
-from ..utils cimport bytes2str
+from ..utils import bytes2str,str2bytes
+from .config    cimport getConfiguration 
+
 
 cdef class ProgressBar:
     cdef clock_t clock(self):
@@ -23,7 +25,7 @@ cdef class ProgressBar:
 
     def __init__(self,
                  off_t maxi,
-                 dict  config,
+                 dict  config={},
                  str head="",
                  double seconde=0.1):
         self.starttime = self.clock()
@@ -34,14 +36,18 @@ cdef class ProgressBar:
         self.arrow     = 0
         self.lastlog   = 0
         
+        if not config:
+            config=getConfiguration()
+            
+        
         self.ontty = sys.stderr.isatty()
         
         if (maxi<=0):
             maxi=1
             
         self.maxi = maxi
-        self.head = str2bytes(head)
+        self._head = str2bytes(head)
-        self.chead= self.head 
+        self.chead= self._head 
         
         
         self.logger=config[config["__root_config__"]]["logger"]
@@ -104,35 +110,43 @@ cdef class ProgressBar:
             if self.ontty:
                 fraction=<int>(percent * 50.)
                 self.arrow=(self.arrow+1) % 4
-                self.diese[fraction]=0
-                self.spaces[50 - fraction]=0
             
                 if days:
-                    <void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %d days %02d:%02d:%02d',
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %d days %02d:%02d:%02d',
                                     self.chead,
                                     percent*100,
-                                    self.diese,self.wheel[self.arrow],self.spaces,
+                                    fraction,self.diese,
+                                    self.wheel[self.arrow],
+                                    50-fraction,self.spaces,
                                     days,hour,minu,sec)
                 else:
-                    <void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %02d:%02d:%02d',
+                    <void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %02d:%02d:%02d',
                                     self.chead,
                                     percent*100.,
-                                    self.diese,self.wheel[self.arrow],self.spaces,
+                                    fraction,self.diese,
+                                    self.wheel[self.arrow],
+                                    50-fraction,self.spaces,
                                     hour,minu,sec)
-                self.diese[fraction]=b'#'
-                self.spaces[50 - fraction]=b' '
 
-            twentyth = int(percent * 20)
+            tenth = int(percent * 10)
-            if twentyth != self.lastlog:
+            if tenth != self.lastlog:
                 
                 if self.ontty:
                     <void>fputs(b'\n',stderr)
                     
                 self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d' % (
-                                        bytes2str(self.head),
+                                        bytes2str(self._head),
                                         percent*100.,
                                         hour,minu,sec))
-                self.lastlog=twentyth
+                self.lastlog=tenth
         else:
             self.cycle+=1
 
+    property head:
+    
+        def __get__(self):
+            return self._head
+        
+        def __set__(self,str value):
+            self._head=str2bytes(value)
+            self.chead=self._head

python/obitools3/format/fasta.pxd

@@ -0,0 +1,10 @@
+from ..utils cimport bytes2str
+from .header cimport HeaderFormat
+from cython.view cimport array as cvarray
+
+cdef class FastaFormat:
+
+    cdef HeaderFormat headerFormater
+    
+    cdef size_t  sequenceBufferLength
+    cdef char*   sequenceBuffer

python/obitools3/format/fasta.pyx

@@ -0,0 +1,32 @@
+cimport cython
+from libc.stdlib cimport malloc, free, realloc
+from libc.string cimport strncpy
+
+cdef class FastaFormat:
+	
+	def __init__(self, list tags=[], bint printNAKeys=False):
+		self.headerFormater = HeaderFormat(True,
+										   tags,
+										   printNAKeys)
+		
+	@cython.boundscheck(False)	
+	def __call__(self, dict data):
+		cdef bytes brawseq      = data['sequence']
+		cdef size_t lseq        = len(brawseq)
+		cdef size_t k=0
+		cdef list   lines       = []
+		
+		for k in range(0,lseq,60):
+			lines.append(brawseq[k:(k+60)])
+			
+		brawseq = b'\n'.join(lines)
+		
+		return "%s\n%s" % (self.headerFormater(data),bytes2str(brawseq))
+					
+		
+				
+			
+		
+		
+		
+		

python/obitools3/format/header.pxd

@@ -0,0 +1,7 @@
+cdef class HeaderFormat:
+
+    cdef str    start
+    cdef set    tags
+    cdef bint   printNaKeys
+    cdef size_t headerBufferLength
+    

python/obitools3/format/header.pyx

@@ -0,0 +1,60 @@
+
+cdef class HeaderFormat:
+    
+    def __init__(self, bint fastaHeader=True, list tags=[], bint printNAKeys=False):
+        '''
+        
+            @param fastaHeader: 
+            @type  fastaHeader: `bool`
+            
+            @param tags:
+            @type  tags: `list` of `bytes`
+            
+            @param printNAKeys: 
+            @type  printNAKeys: `bool` 
+        '''
+        
+        self.tags           = set(tags)
+        self.printNaKeys    = printNAKeys
+        
+        if fastaHeader:
+            self.start=">"
+        else:
+            self.start="@"
+        
+        self.headerBufferLength = 1000
+        #self.headerBuffer = []
+        
+    def __call__(self, dict data):
+        cdef str header
+        cdef dict tags = data['tags']
+        cdef set  ktags
+        cdef list lines = [""]
+        cdef str tagline
+        
+        if self.tags is not None and self.tags:
+            ktags = self.tags
+        else:
+            ktags = set(tags.keys())
+            
+        for k in ktags:
+            if k in tags:
+                value = tags[k]
+                if value is not None or self.printNaKeys:
+                    lines.append("%s=%s;" % (k,tags[k]))
+                    
+        if len(lines) > 1:
+            tagline=" ".join(lines)
+        else:
+            tagline=""
+            
+        if data['definition'] is not None:
+            header = "%s%s%s %s" % (self.start,data['id'],
+                                    tagline,
+                                    data['definition'])
+        else:
+            header = "%s%s%s" % (self.start,data['id'],
+                                 tagline)
+            
+        return header
+        

python/obitools3/obidms/_obidmscolumn_seq.pyx

@@ -26,17 +26,26 @@ cdef class OBIDMS_column_seq(OBIDMS_column):
         if value == OBISeq_NA :
             result = None
         else :
-            result = bytes2str(value)
+            try:
-            free(value)
+                result = <bytes> value
+            finally:
+                free(value)
         return result
 
     cpdef set_line(self, index_t line_nb, object value):
+        cdef bytes value_b
+
         if value is None :
-            if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, OBISeq_NA) < 0:
+            value_b = OBISeq_NA
-                raise Exception("Problem setting a value in a column")
+        elif isinstance(value, bytes) :
-        else :
+            value_b = value
-            if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, str2bytes(value)) < 0:
+        elif isinstance(value, str) :
-                raise Exception("Problem setting a value in a column")
+            value_b = str2bytes(value)
+        else:
+            raise TypeError('Sequence value must be of type Bytes, Str or None')
+
+        if obi_set_seq_with_elt_idx_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, 0, value_b) < 0:
+            raise Exception("Problem setting a value in a column")
         
 
 cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
@@ -50,10 +59,13 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
         if value == OBISeq_NA :
             result = None
         else :
-            result = bytes2str(value)
+            try:
-            free(value)
+                result = <bytes> value
+            finally:
+                free(value)
         return result
 
+    
     cpdef object get_line(self, index_t line_nb) :
         cdef char*   value
         cdef object  value_in_result
@@ -69,8 +81,10 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
             if value == OBISeq_NA :
                 value_in_result = None
             else :
-                value_in_result = bytes2str(value)
+                try:
-                free(value)    
+                    value_in_result = <bytes> value
+                finally:
+                    free(value)    
             result[self.elements_names[i]] = value_in_result
             if all_NA and (value_in_result is not None) :
                 all_NA = False
@@ -92,7 +106,4 @@ cdef class OBIDMS_column_multi_elts_seq(OBIDMS_column_multi_elts):
         
         if obi_set_seq_with_elt_name_and_col_p_in_view(self.view.pointer, (self.pointer)[0], line_nb, str2bytes(element_name), value_b) < 0:
             raise Exception("Problem setting a value in a column")
-    
-#    cpdef align(self, ):        # TODO
-#        raise Exception("Columns with multiple sequences per line can't be aligned")    # TODO discuss
 

python/obitools3/parsers/fasta.pxd

@@ -1,5 +1,6 @@
 #cython: language_level=3
 
+from ..utils cimport str2bytes
 from .header cimport parseHeader
 from ..files.universalopener cimport uopen
 from ..files.linebuffer cimport LineBuffer

python/obitools3/parsers/fasta.pyx

@@ -6,12 +6,15 @@ Created on 30 mars 2016
 @author: coissac
 '''
 
+
 def fastaIterator(lineiterator, int buffersize=100000000):
     cdef LineBuffer lb
     cdef str        ident
     cdef str        definition
     cdef dict       tags
     cdef list       s
+    cdef bytes      sequence
+    cdef bytes      quality
     
     if isinstance(lineiterator,(str,bytes)):
         lineiterator=uopen(lineiterator)
@@ -31,12 +34,12 @@ def fastaIterator(lineiterator, int buffersize=100000000):
         
         try:
             while line[0]!='>':
-                s.append(line[0:-1])
+                s.append(str2bytes(line)[0:-1])
                 line = next(i)
         except StopIteration:
             pass
         
-        sequence  = "".join(s)
+        sequence  = b"".join(s)
         quality   = None
 
         yield { "id"         : ident,

python/obitools3/parsers/fastq.pxd

@@ -1,5 +1,7 @@
 #cython: language_level=3
 
+from ..utils cimport str2bytes
+
 from .header cimport parseHeader
 from ..files.universalopener cimport uopen
 from ..files.linebuffer cimport LineBuffer

python/obitools3/parsers/fastq.pyx

@@ -6,15 +6,13 @@ Created on 30 mars 2016
 @author: coissac
 '''
 
-
-
-
-
 def fastqIterator(lineiterator, int buffersize=100000000):
     cdef LineBuffer lb
     cdef str        ident
     cdef str        definition
     cdef dict       tags
+    cdef bytes      sequence
+    cdef bytes      quality
     
     if isinstance(lineiterator,(str,bytes)):
         lineiterator=uopen(lineiterator)
@@ -27,9 +25,9 @@ def fastqIterator(lineiterator, int buffersize=100000000):
     i = iter(lb)
     for line in i:
         ident,tags,definition = parseHeader(line)
-        sequence  = next(i)[0:-1]
+        sequence  = str2bytes(next(i)[0:-1])
         next(i)
-        quality   = next(i)[0:-1]
+        quality   = str2bytes(next(i)[0:-1])
 
         yield { "id"         : ident,
                 "definition" : definition,

requirements.txt

@@ -1,5 +1,5 @@
 --extra-index-url https://pypi.python.org/simple/
-Cython==0.23.5
+Cython>=0.24
 Sphinx>=1.2.0
 ipython>=3.0.0
 breathe>=4.0.0