--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phrap/jgi_assembly.py	Tue Jun 07 17:41:56 2011 -0400
@@ -0,0 +1,117 @@
+"""
+Assembly classes
+"""
+
+import data
+import logging
+import re
+import string
+from cgi import escape
+from galaxy.datatypes.metadata import MetadataElement
+from galaxy.datatypes import metadata
+import galaxy.model
+from galaxy import util
+from sniff import *
+
+log = logging.getLogger(__name__)
+
+class Assembly( data.Text ):
+    """Class describing an assembly"""
+
+    """Add metadata elements"""
+    MetadataElement( name="contigs", default=0, desc="Number of contigs", readonly=True, visible=False, optional=True, no_value=0 )
+    MetadataElement( name="reads", default=0, desc="Number of reads", readonly=True, visible=False, optional=True, no_value=0 )
+
+
+class Ace(Assembly):
+    """Class describing an assembly Ace file"""
+
+    file_ext = "ace"
+
+#    def init_meta( self, dataset, copy_from=None ):
+#        Assembly.init_meta( self, dataset, copy_from=copy_from )
+
+    def set_meta( self, dataset, overwrite=True, **kwd ):
+        """
+        Set the number of assembled contigs and read sequences and the number of data lines in dataset.
+        """
+        contigs = 0
+        reads = 0
+        for line in file( dataset.file_name ):
+            line = line.strip()
+            if line and line.startswith( '#' ):
+                # Don't count comment lines
+                continue
+            if line and line.startswith( 'CO' ):
+                contigs += 1
+            if line and line.startswith( 'RD' ):
+                reads += 1
+        dataset.metadata.contigs = contigs
+        dataset.metadata.reads = reads
+
+    def set_peek( self, dataset, is_multi_byte=False ):
+        if not dataset.dataset.purged:
+            dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte )
+            if dataset.metadata.contigs:
+                dataset.blurb = "%s contigs" % util.commaify( str( dataset.metadata.contigs ) )
+            else:
+                dataset.blurb = data.nice_size( dataset.get_size() )
+        else:
+            dataset.peek = 'file does not exist'
+            dataset.blurb = 'file purged from disk'
+
+    def sniff( self, filename ):
+        """
+        Determines whether the file is in ace format
+
+        An ace file contains these sections 
+        AS  \d+ \d+
+
+        CO \S+ \d+ \d+ \d+ \w
+        [atcgATCGN\*]+
+
+        BQ
+        [\d\s]+
+
+        AF \S+ [CU] \-?\d+
+
+        BS \d+ \d+ \S+
+
+        RD \S+ \d+ \d+ \d+
+        [ATCGN\*]+
+
+        QA \d+ \d+ \d+ \d+
+        DS .*
+
+        Currently we only check if file begins with AS
+
+        >>> fname = get_test_fname( 'genome.ace' )
+        >>> Ace().sniff( fname )
+        True
+        >>> fname = get_test_fname( 'genome.fasta' )
+        >>> Ace().sniff( fname )
+        False
+        """
+
+        try:
+            fh = open( filename )
+            line = fh.readline()
+            line = line.strip()
+            if line:
+                if line.startswith( 'AS ' ):
+                    fh.close()
+                    return True
+            fh.close()
+            return False
+        except:
+            pass
+        return False
+
+class Velveth(Assembly):
+    composite_type='basic'
+    file_ext = "txt"
+
+    def __init__(self,**kwd):
+        Assembly.__init__(self,**kwd)
+        self.add_composite_file('Roadmap')
+        self.add_composite_file('Sequences')