# cython: embedsignature=True
# adds doc-strings for sphinx
-import tempfile, os, sys, types, itertools, struct, ctypes
+import tempfile, os, sys, types, itertools, struct, ctypes, gzip
+from cpython cimport PyString_FromStringAndSize, PyString_AS_STRING
+cimport TabProxies
cdef class Tabixfile:
'''*(filename, mode='r')*
index (*filename* + ".tbi") will raise an exception.
'''
- cdef char * filename
-
- # pointer to tabixfile
- cdef tabix_t * tabixfile
-
def __cinit__(self, *args, **kwargs ):
self.tabixfile = NULL
self._open( *args, **kwargs )
else:
return TabixIteratorParsed( self, -1, 0, 0, parser )
+ property header:
+ 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:
- '''chromosome names'''
- def __get__(self):
- cdef char ** sequences
- cdef int nsequences
+ '''chromosome names'''
+ def __get__(self):
+ cdef char ** sequences
+ cdef int nsequences
- ti_lazy_index_load( self.tabixfile )
- sequences = ti_seqname( self.tabixfile.idx, &nsequences )
- cdef int x
- result = []
- for x from 0 <= x < nsequences:
- result.append( sequences[x] )
- return result
+ ti_lazy_index_load( self.tabixfile )
+ sequences = ti_seqname( self.tabixfile.idx, &nsequences )
+ cdef int x
+ result = []
+ for x from 0 <= x < nsequences:
+ result.append( sequences[x] )
+ return result
cdef class TabixIterator:
"""iterates over rows in *tabixfile* in region
cdef char * s
cdef int len
- s = ti_read(self.tabixfile, self.iterator, &len)
- if s == NULL: raise StopIteration
+ # metachar filtering does not work within tabix
+ # though it should. Getting the metachar is a pain
+ # as ti_index_t is incomplete type.
+
+ # simply use '#' for now.
+ while 1:
+ s = ti_read(self.tabixfile, self.iterator, &len)
+ if s == NULL: raise StopIteration
+ if s[0] != '#': break
+
return s
def __dealloc__(self):
if <void*>self.iterator != NULL:
ti_iter_destroy(self.iterator)
-def toDot( v ):
- '''convert value to '.' if None'''
- if v == None: return "."
- else: return str(v)
-
-def quote( v ):
- '''return a quoted attribute.'''
- if type(v) in types.StringTypes:
- return '"%s"' % v
- else:
- return str(v)
-
-cdef class TupleProxy:
- '''Proxy class for access to parsed row as a tuple.
-
- This class represents a table row for fast read-access.
- '''
-
- cdef:
- char * data
- char ** fields
- int nfields
- int index
-
- def __cinit__(self ):
-
- self.data = NULL
- self.fields = NULL
- self.index = 0
-
- cdef take( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take ownership of the pointer.
- '''
- self.data = buffer
- self.update( buffer, nbytes )
-
- cdef present( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Do not take ownership of the pointer.
- '''
- self.update( buffer, nbytes )
-
- cdef copy( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
+cdef class TabixHeaderIterator:
+ """return header lines.
+ """
+
+ cdef ti_iter_t iterator
+ cdef tabix_t * tabixfile
- Take a copy of buffer.
- '''
- cdef int s
- # +1 for '\0'
- s = sizeof(char) * (nbytes + 1)
- self.data = <char*>malloc( s )
- memcpy( <char*>self.data, buffer, s )
- self.update( self.data, nbytes )
-
- cdef update( self, char * buffer, size_t nbytes ):
- '''update internal data.'''
- cdef char * pos
- cdef char * old_pos
- cdef int field
- cdef int max_fields
- field = 0
-
- if buffer[nbytes] != 0:
- raise ValueError( "incomplete line at %s" % buffer )
+ def __cinit__(self, Tabixfile tabixfile ):
- if self.fields != NULL:
- free(self.fields)
-
- max_fields = nbytes / 4
- self.fields = <char **>calloc( max_fields, sizeof(char *) )
-
- pos = buffer
- self.fields[0] = pos
- field += 1
- old_pos = pos
+ assert tabixfile._isOpen()
- while 1:
-
- pos = <char*>memchr( pos, '\t', nbytes )
- if pos == NULL: break
- pos[0] = '\0'
- pos += 1
- self.fields[field] = pos
- field += 1
- if field >= max_fields:
- raise ValueError("row too large - more than %i fields" % max_fields )
- nbytes -= pos - old_pos
- if nbytes < 0: break
- old_pos = pos
-
- self.nfields = field
-
- def __getitem__( self, key ):
-
- cdef int i
- i = key
- if i < 0: i += self.nfields
- if i >= self.nfields or i < 0:
- raise IndexError( "list index out of range" )
- return self.fields[i]
+ # makes sure that samfile stays alive as long as the
+ # iterator is alive.
+ self.tabixfile = tabixfile.tabixfile
- def __len__(self):
- return self.nfields
+ self.iterator = ti_query(self.tabixfile, NULL, 0, 0)
- def __dealloc__(self):
- if self.data != NULL:
- free(self.data)
+ if <void*>self.iterator == NULL:
+ raise ValueError("can't open header.\n")
def __iter__(self):
- self.index = 0
- return self
+ return self
def __next__(self):
"""python version of next().
- """
- if self.index >= self.nfields:
- raise StopIteration
- self.index += 1
- return self.fields[self.index-1]
-cdef class GTFProxy:
- '''Proxy class for access to GTF fields.
-
- This class represents a GTF entry for fast read-access.
- Write-access has been added as well, though some care must
- be taken. If any of the string fields (contig, source, ...)
- are set, the new value is tied to the lifetime of the
- argument that was supplied.
-
- The only exception is the attributes field when set from
- a dictionary - this field will manage its own memory.
-
- '''
-
- cdef:
- char * contig
- char * source
- char * feature
- uint32_t start
- uint32_t end
- char * score
- char * strand
- char * frame
- char * attributes
- int nbytes
- char * data
- cdef bint isModified
- cdef bint hasOwnAttributes
-
- def __cinit__(self ):
- self.data = NULL
- self.isModified = False
- self.hasOwnAttributes = False
-
- cdef take( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take ownership of the pointer.
- '''
- self.data = buffer
- self.update( buffer, nbytes )
- self.isModified = False
-
- cdef present( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Do not take ownership of the pointer.
- '''
- self.update( buffer, nbytes )
- self.isModified = False
-
- cdef copy( self, char * buffer, size_t nbytes ):
- '''start presenting buffer.
-
- Take a copy of buffer.
- '''
- cdef int s
- # +1 for '\0'
- s = sizeof(char) * (nbytes + 1)
- self.data = <char*>malloc( s )
- memcpy( <char*>self.data, buffer, s )
- self.update( self.data, nbytes )
- self.isModified = False
-
- cdef update( self, char * buffer, size_t nbytes ):
- '''update internal data.
-
- nbytes does not include the terminal '\0'.
- '''
- cdef int end
- cdef char * cstart, * cend, * cscore
- self.contig = buffer
- self.nbytes = nbytes
- cdef char * pos
-
- if buffer[nbytes] != 0:
- raise ValueError( "incomplete line at %s" % buffer )
-
- pos = strchr( buffer, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.source = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.feature = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- cstart = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- cend = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.score = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.strand = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.frame = pos
-
- pos = strchr( pos, '\t' )
- if pos == NULL: raise ValueError( "malformatted entry at %s" % buffer )
- pos[0] = '\0'
- pos += 1
- self.attributes = pos
- self.start = atoi( cstart ) - 1
- self.end = atoi( cend )
-
- property contig:
- '''contig of feature.'''
- def __get__( self ): return self.contig
- def __set__( self, value ):
- self.isModified = True
- self.contig = value
-
- property feature:
- '''feature name.'''
- def __get__( self ): return self.feature
- def __set__( self, value ):
- self.isModified = True
- self.feature = value
-
- property source:
- '''feature source.'''
- def __get__( self ): return self.source
- def __set__( self, value ):
- self.isModified = True
- self.source = value
-
- property start:
- '''feature start (in 0-based open/closed coordinates).'''
- def __get__( self ): return self.start
- def __set__( self, value ):
- self.isModified = True
- self.start = value
-
- property end:
- '''feature end (in 0-based open/closed coordinates).'''
- def __get__( self ): return self.end
- def __set__( self, value ):
- self.isModified = True
- self.end = value
-
- property score:
- '''feature score.'''
- def __get__( self ):
- if self.score[0] == '.' and self.score[1] == '\0' :
- return None
- else:
- return atof(self.score)
- def __set__( self, value ):
- self.isModified = True
- self.score = value
-
- property strand:
- '''feature strand.'''
- def __get__( self ): return self.strand
- def __set__( self, value ):
- self.isModified = True
- self.strand = value
-
- property frame:
- '''feature frame.'''
- def __get__( self ): return self.frame
- def __set__( self, value ):
- self.isModified = True
- self.frame = value
-
- property attributes:
- '''feature attributes (as a string).'''
- def __get__( self ): return self.attributes
- def __set__( self, value ):
- self.isModified = True
- self.attributes = value
-
- def asDict( self ):
- """parse attributes - return as dict
+ pyrex uses this non-standard name instead of next()
"""
-
- # remove comments
- attributes = self.attributes
-
- # separate into fields
- fields = [ x.strip() for x in attributes.split(";")[:-1]]
-
- result = {}
-
- for f in fields:
-
- d = [ x.strip() for x in f.split(" ")]
-
- n,v = d[0], d[1]
- if len(d) > 2: v = d[1:]
-
- if v[0] == '"' and v[-1] == '"':
- v = v[1:-1]
- else:
- ## try to convert to a value
- try:
- v = float( v )
- v = int( v )
- except ValueError:
- pass
- except TypeError:
- pass
-
- result[n] = v
-
- return result
- def fromDict( self, d ):
- '''set attributes from a dictionary.'''
- cdef char * p
- cdef int l
-
- # clean up if this field is set twice
- if self.hasOwnAttributes:
- free(self.attributes)
-
- aa = []
- for k,v in d.items():
- if type(v) == types.StringType:
- aa.append( '%s "%s"' % (k,v) )
- else:
- aa.append( '%s %s' % (k,str(v)) )
-
- a = "; ".join( aa ) + ";"
- p = a
- l = len(a)
- self.attributes = <char *>calloc( l + 1, sizeof(char) )
- memcpy( self.attributes, p, l )
-
- self.hasOwnAttributes = True
- self.isModified = True
-
- def __str__(self):
- cdef char * cpy
- cdef int x
-
- if self.isModified:
- return "\t".join(
- (self.contig,
- self.source,
- self.feature,
- str(self.start+1),
- str(self.end),
- toDot(self.score),
- self.strand,
- self.frame,
- self.attributes ) )
- else:
- cpy = <char*>calloc( sizeof(char), self.nbytes+1 )
- memcpy( cpy, self.data, self.nbytes+1)
- for x from 0 <= x < self.nbytes:
- if cpy[x] == '\0': cpy[x] = '\t'
- result = cpy
- free(cpy)
- return result
-
- def invert( self, int lcontig ):
- '''invert coordinates to negative strand coordinates
-
- This method will only act if the feature is on the
- negative strand.'''
-
- if self.strand[0] == '-':
- start = min(self.start, self.end)
- end = max(self.start, self.end)
- self.start, self.end = lcontig - end, lcontig - start
+ cdef char * s
+ cdef int len
- def keys( self ):
- '''return a list of attributes defined in this entry.'''
- r = self.attributes
- return [ x.strip().split(" ")[0] for x in r.split(";") if x.strip() != '' ]
+ # Getting the metachar is a pain as ti_index_t is incomplete type.
+ # simply use '#' for now.
+ s = ti_read(self.tabixfile, self.iterator, &len)
+ if s == NULL: raise StopIteration
+ # stop at first non-header line
+ if s[0] != '#': raise StopIteration
- def __getitem__(self, item):
- return self.__getattr__( item )
+ return s
def __dealloc__(self):
- if self.data != NULL:
- free(self.data)
- if self.hasOwnAttributes:
- free(self.attributes)
-
- def __getattr__(self, item ):
- """Generic lookup of attribute from GFF/GTF attributes
- Only called if there *isn't* an attribute with this name
- """
- cdef char * start
- cdef char * query
- cdef char * cpy
- cdef char * end
- cdef int l
- query = item
-
- start = strstr( self.attributes, query)
- if start == NULL:
- raise AttributeError("'GTFProxy' has no attribute '%s'" % item )
-
- start += strlen(query) + 1
- # skip gaps before
- while start[0] == " ": start += 1
- if start[0] == '"':
- start += 1
- end = start
- while end[0] != '\0' and end[0] != '"': end += 1
- l = end - start + 1
- cpy = <char*>calloc( l, sizeof(char ) )
- memcpy( cpy, start, l )
- cpy[l-1] = '\0'
- result = cpy
- free(cpy)
- return result
- else:
- return start
-
- def setAttribute( self, name, value ):
- '''convenience method to set an attribute.'''
- r = self.asDict()
- r[name] = value
- self.fromDict( r )
+ if <void*>self.iterator != NULL:
+ ti_iter_destroy(self.iterator)
+#########################################################
+#########################################################
+#########################################################
cdef class Parser:
pass
cdef class asTuple(Parser):
'''converts a :term:`tabix row` into a python tuple.'''
def __call__(self, char * buffer, int len):
- cdef TupleProxy r
- r = TupleProxy()
+ cdef TabProxies.TupleProxy r
+ r = TabProxies.TupleProxy()
# need to copy - there were some
# persistence issues with "present"
r.copy( buffer, len )
cdef class asGTF(Parser):
'''converts a :term:`tabix row` into a GTF record.'''
def __call__(self, char * buffer, int len):
- cdef GTFProxy r
- r = GTFProxy()
+ cdef TabProxies.GTFProxy r
+ r = TabProxies.GTFProxy()
r.copy( buffer, len )
return r
+cdef class asBed( Parser ):
+ '''converts a :term:`tabix row` into a GTF record.'''
+ def __call__(self, char * buffer, int len):
+ cdef TabProxies.BedProxy r
+ r = TabProxies.BedProxy()
+ r.copy( buffer, len )
+ return r
+
+cdef class asVCF( Parser ):
+ '''converts a :term:`tabix row` into a VCF record.'''
+ def __call__(self, char * buffer, int len ):
+ cdef TabProxies.VCFProxy r
+ r = TabProxies.VCFProxy()
+ r.copy( buffer, len )
+ return r
+
+#########################################################
+#########################################################
+#########################################################
cdef class TabixIteratorParsed:
"""iterates over mapped reads in a region.
+
+ Returns parsed data.
"""
-
+
cdef ti_iter_t iterator
cdef tabix_t * tabixfile
cdef Parser parser
cdef char * s
cdef int len
- s = ti_read(self.tabixfile, self.iterator, &len)
- if s == NULL: raise StopIteration
+ while 1:
+ s = ti_read(self.tabixfile, self.iterator, &len)
+ if s == NULL: raise StopIteration
+ # todo: read metachar from configuration
+ if s[0] != '#': break
+
return self.parser(s, len)
def __dealloc__(self):
"Tabixfile",
"asTuple",
"asGTF",
+ "asVCF",
+ "asBed",
]
projects / pysam.git / blobdiff