Merge branch 'Eric_version_for_sequence'

Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx

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")
     
     # TODO choose alignment type (lcs or other) with supplementary argument
     cpdef align(self, 
@@ -62,10 +71,13 @@ 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
@@ -81,8 +93,10 @@ 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

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,