--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reference_bins.py	Mon Mar 02 20:46:00 2015 -0500
@@ -0,0 +1,148 @@
+import os.path
+import common
+
+class ReferenceBins:
+
+	def __init__(self, db_spec_path = None):
+		"""
+	 	@param db_spec_path string path to fasta databases specification file.  This file has format:
+		 #value	id	type	active	name	path
+		 16S_euzby	16S	1	Euzby	/usr/local/galaxy/shared/ngs_data/
+		 ...
+		"""
+		self.reference_bins = []
+
+		if db_spec_path == None: # Default to the command-line lookup table in code's folder: 
+			db_spec_path = os.path.join(os.path.dirname(__file__), 'fasta_reference_dbs.tab') 	
+		self.fieldSpec = common.FieldSpec(db_spec_path)
+
+	def __main__(self): pass
+	
+	# Could double check to see if it exists?
+	def build_bins(self, bins, columns):
+				
+		if bins == None: 
+			self.reference_bins = []		
+			return False
+			
+		for myfield in bins.strip().strip(';').split(';'):
+			field_spec = myfield.strip().split(':')
+			field_name = field_spec[0].strip()
+
+			if field_name != '':
+				if not field_name.replace('_','').isalnum():
+					common.stop_err("Invalid bin name: " + field_name + ':' + myfield)
+				
+				if len(field_spec) < 2: field_spec.append('column') # default grouping = column
+				if len(field_spec) < 3: field_spec.append('') # default filtering = none
+				if len(field_spec) < 4: field_spec.append('') # default no description
+
+				grouping = field_spec[1].strip()
+				if not grouping in ['table', 'column', 'hidden']:
+					common.stop_err("Invalid bin layout: " + grouping)
+
+				bin_filter = field_spec[2].strip()
+				if not bin_filter in ['', 'include', 'exclude']:
+					common.stop_err("Invalid bin sort: " + bin_filter)
+
+				newbin = self.buildBin(field_name, bin_filter)
+				self.reference_bins.append(newbin)				
+				
+				field = { # any time we have a bin we want sort descending
+					'field': field_name,
+					'group': grouping,
+					'sort': 'desc',
+					'label': newbin.name,
+					'type': 'bin'
+				} 
+				columns.append(field)
+				if (field_spec[3] == 'true'): # description field requested
+					field = {
+						'field': field_name + '_desc',
+						'group': 'column',
+						'sort': '',							# Allow other sorts????
+						'label': newbin.name + ' Description',
+						'type': 'text'
+					} 
+					columns.append(field)
+
+
+	def buildBin(self, bin_folder_name, bin_filter):
+		""" 
+		 Create a lookup table consisting of a dictionary entry for each accession id held in dictionary's file.
+		 @param bin_folder_name string name of requested db, e.g 16S_ncbi 
+		 @param bin_filter string '' or 'include' or 'exclude'
+	
+		"""
+		bin = ReferenceBin(self.fieldSpec, bin_folder_name, bin_filter)
+		
+		try:
+			with open(bin.file_path) as file_in:
+				for line in file_in: # Should always contains succession id
+					#FUTURE: Preprocess so accession ID ready to go.
+					keyValue = line.rstrip().split("\t",1)
+ 					# keep only first term minus integer portion of id
+					accGeneralId = keyValue[0].split('.')[0]
+					if len(keyValue) >1: description = keyValue[1]
+					else: description = ''
+					bin.lookup[accGeneralId] = description
+				
+				file_in.close()
+			
+		except IOError:
+		   stop_err("Reference bin could not be found or opened: " + self.path + bin_folder_name + '/accession_ids.tab')
+		
+		return bin
+
+	def setStatus(self, record):
+
+		if len(self.reference_bins) == 0: return #no bins
+
+		# Use of "extended slices" http://docs.python.org/2.3/whatsnew/section-slices.html
+		# Example sallseqid is 'gi|194753780|ref|XR_046072.1|;gi|195119578|ref|XR_047594.1|;gi|195154052|ref|XR_047967.1|'
+ 		# Example accs is ['XR_046072.1', 'XR_047594.1', 'XR_047967.1']
+		# Original code was "[1::2][1::2]" (select every 2nd item, then every 2nd item of that)
+		accs = record.sallseqid.split('|')
+
+		if common.re_default_ncbi_id.match(record.sseqid):
+			accs = accs[3::4] #Select every 4th item starting offset 4
+			
+		elif common.re_default_ref_id.match(record.sseqid):
+			accs = accs[1::2]
+		
+
+		# Check each accession # against each bin.  
+		for ptr, bin in enumerate(self.reference_bins):		
+				setattr(record, bin.field, '') #Using '','1' not FALSE/TRUE because of tab delim output
+				setattr(record, bin.field + '_desc', '')			
+				for acc in accs:
+					accGeneralId = acc.split('.')[0]
+					if accGeneralId in bin.lookup:
+						if bin.exclude: return False
+						setattr(record, bin.field, str(ptr+1))
+						# Include any bin notes for this item
+						setattr(record, bin.field + '_desc', bin.lookup[accGeneralId])
+						break # This result has been binned to this bin so break.
+
+
+
+
+	def __str__(self):
+		return "name: %s    dict: %s" % (self.name, str(self.lookup))
+
+class ReferenceBin: 
+	def __init__(self, fieldSpec, bin_folder_name, bin_filter):
+		self.lookup = {}
+		self.folder = bin_folder_name
+		self.name = fieldSpec.getAttribute(bin_folder_name, 'name')
+		self.field = bin_folder_name
+		self.path = fieldSpec.getAttribute(bin_folder_name, 'path')
+		self.exclude = bin_filter
+		#absolute path to reference bins folder: /usr/local/galaxy/shared/ngs_data/
+		self.file_path = os.path.join(self.path + self.folder + '/accession_ids.tab')
+		
+if __name__ == '__main__':
+
+        binManager = ReferenceBins()
+        binManager.__main__()
+