Imported Upstream version 0.5

[pysam.git] / pysam / ctabix.pyx

diff --git a/pysam/ctabix.pyx b/pysam/ctabix.pyx
index a31f3f244b37329286cc23760d5c2942b8628103..25c1a1ee732df3e383a29e80c1ea2ae533b7925e 100644 (file)
--- a/pysam/ctabix.pyx
+++ b/pysam/ctabix.pyx
@@ -33,9 +33,7 @@ cdef class Tabixfile:
         if self.tabixfile != NULL: self.close()
         self.tabixfile = NULL
 
-        if self._filename != NULL: free(self._filename )
-        self._filename = strdup( filename )
-
+        self.filename = filename
         filename_index = filename + ".tbi"
 
         if mode[0] == 'w':
@@ -44,14 +42,14 @@ cdef class Tabixfile:
 
         elif mode[0] == "r":
             # open file for reading
-            if not os.path.exists( self._filename ):
-                raise IOError( "file `%s` not found" % self._filename)
+            if not os.path.exists( self.filename ):
+                raise IOError( "file `%s` not found" % self.filename)
 
             if not os.path.exists( filename_index ):
                 raise IOError( "index `%s` not found" % filename_index)
 
             # open file and load index
-            self.tabixfile = ti_open( self._filename, filename_index )
+            self.tabixfile = ti_open( self.filename, filename_index )
 
         if self.tabixfile == NULL:
             raise IOError("could not open file `%s`" % filename )
@@ -138,26 +136,12 @@ cdef class Tabixfile:
             else:
                 return TabixIteratorParsed( self, -1, 0, 0, parser )
 
-    ###############################################################
-    ###############################################################
-    ###############################################################
-    ## properties
-    ###############################################################
-    property filename:
-        '''filename associated with this object.'''
-        def __get__(self):
-            if not self._isOpen(): raise ValueError( "I/O operation on closed file" )
-            return self._filename
-
     property header:
-        '''the file header.
-          
-        .. note::
-            The header is returned as an iterator over lines without the
-            newline character.
-        '''
-        
         def __get__( self ):
+            '''return header lines as an iterator.
+
+            Note that the header lines do not contain the newline '\n' character.
+            '''
             return TabixHeaderIterator( self )
 
     property contigs:
@@ -174,22 +158,6 @@ cdef class Tabixfile:
                 result.append( sequences[x] )
             return result
             
-    def close( self ):
-        '''
-        closes the :class:`pysam.Tabixfile`.'''
-        if self.tabixfile != NULL:
-            ti_close( self.tabixfile )
-            self.tabixfile = NULL
-
-    def __dealloc__( self ):
-        # remember: dealloc cannot call other python methods
-        # note: no doc string
-        # note: __del__ is not called.
-        if self.tabixfile != NULL:
-            ti_close( self.tabixfile )
-            self.tabixfile = NULL
-        if self._filename != NULL: free( self._filename )
-
 cdef class TabixIterator:
     """iterates over rows in *tabixfile* in region
     given by *tid*, *start* and *end*.
@@ -297,10 +265,7 @@ cdef class Parser:
     pass
 
 cdef class asTuple(Parser):
-    '''converts a :term:`tabix row` into a python tuple.
-
-    Access is by numeric index.
-    ''' 
+    '''converts a :term:`tabix row` into a python tuple.''' 
     def __call__(self, char * buffer, int len):
         cdef TabProxies.TupleProxy r
         r = TabProxies.TupleProxy()
@@ -310,36 +275,7 @@ cdef class asTuple(Parser):
         return r
 
 cdef class asGTF(Parser):
-    '''converts a :term:`tabix row` into a GTF record with the following 
-    fields:
-
-    contig
-       contig
-    feature
-       feature
-    source
-       source
-    start
-       genomic start coordinate (0-based)
-    end
-       genomic end coordinate plus one (0-based)
-    score
-       feature score
-    strand
-       strand
-    frame
-       frame
-    attributes
-       attribute string.
-
-    GTF formatted entries also defined the attributes:
-
-    gene_id
-       the gene identifier
-    transcript_ind
-       the transcript identifier
-    
-    ''' 
+    '''converts a :term:`tabix row` into a GTF record.''' 
     def __call__(self, char * buffer, int len):
         cdef TabProxies.GTFProxy r
         r = TabProxies.GTFProxy()
@@ -347,39 +283,7 @@ cdef class asGTF(Parser):
         return r
 
 cdef class asBed( Parser ):
-    '''converts a :term:`tabix row` into a bed record
-    with the following fields:
-
-    contig
-       contig
-    start
-       genomic start coordinate (zero-based)
-    end
-       genomic end coordinate plus one (zero-based)
-    name
-       name of feature.
-    score
-       score of feature
-    strand
-       strand of feature
-    thickStart
-       thickStart
-    thickEnd
-       thickEnd
-    itemRGB
-       itemRGB
-    blockCount
-       number of bocks
-    blockSizes
-       ',' separated string of block sizes
-    blockStarts
-       ',' separated string of block genomic start positions
-
-    Only the first three fields are required. Additional
-    fields are optional, but if one is defined, all the preceeding
-    need to be defined as well.
-
-    ''' 
+    '''converts a :term:`tabix row` into a GTF record.''' 
     def __call__(self, char * buffer, int len):
         cdef TabProxies.BedProxy r
         r = TabProxies.BedProxy()
@@ -387,35 +291,7 @@ cdef class asBed( Parser ):
         return r
 
 cdef class asVCF( Parser ): 
-    '''converts a :term:`tabix row` into a VCF record with
-    the following fields:
-    
-    contig
-       contig
-    pos
-       chromosomal position, zero-based
-    id 
-       id
-    ref
-       reference
-    alt
-       alt
-    qual
-       qual
-    filter
-       filter
-    info
-       info
-    format
-       format specifier.
-
-    Access to genotypes is via index::
-
-        contig = vcf.contig
-        first_sample_genotype = vcf[0]
-        second_sample_genotype = vcf[1]
-
-    '''
+    '''converts a :term:`tabix row` into a VCF record.'''
     def __call__(self, char * buffer, int len ):
         cdef TabProxies.VCFProxy r
         r = TabProxies.VCFProxy()