LMS-1882 dynamix: script to update metadata from yeastgenome.org

SVN: 18871

screening/source/python/dynamix-orf-update.py

+#!/usr/bin/python
+# Creates an update of the ORF materials for the DynamiX project.
+# The output file has to be imported using material batch update.
+#
+# Before you run this script you have to manually download the list of all ORF codes from openBIS
+# 1. Go to:
+#      http://dynamix.vital-it.ch/openbis/?viewMode=simple#action=BROWSE&entity=MATERIAL&type=ORF
+# 2. Hide all columns instead of "Code" and export the table
+# 3. Save the result in 'used-orfs.txt' file and remove the header
+
+# Author: Tomasz Pylak
+
+
+import os
+
+METADATA_FILE_URL="http://downloads.yeastgenome.org/chromosomal_feature/SGD_features.tab"
+HEADER="PRIMARY_SGD_ID	ORF_CLASSIFICATION	code	STANDARD_NAME	ALIAS_NAMES	CHROMOSOME_STANDARD_NAME	DESCRIPTION"
+NAME_INDEX=2
+ALIAS_INDEX=4
+
+# returns the set of ORFs codes defined in openBIS
+def getUsedCodes(filePath):
+	f = open(filePath)
+	usedCodes = set()
+	for line in f:
+		line = line.strip()
+		if (line[0] == 'Y'):
+			usedCodes.add(line)
+	return usedCodes
+	
+def createUpdate(usedCodes, metadataFile, outFileName):
+	out = open(outFileName, 'w')
+	out.write(HEADER+"\n");
+	importedCodes = set()
+	
+	for line in metadataFile:
+		tokens = line.strip().split('\t')
+		name = tokens[NAME_INDEX]
+		if len(tokens) > ALIAS_INDEX:
+			aliases = set(tokens[ALIAS_INDEX].strip().split('|'))
+		else: 
+			aliases = set()
+		if (name in usedCodes):
+			out.write(line)
+			importedCodes.add(name)
+		if len(aliases & usedCodes) > 0:
+			used_aliases = aliases & usedCodes
+			if len(used_aliases) > 1:
+				raise Exception('Alias matches more name: '+(used_aliases))
+			alias = used_aliases.pop()
+			tokens[NAME_INDEX] = alias
+			tokens[ALIAS_INDEX] = tokens[ALIAS_INDEX]+'|'+name
+			print "Using alias "+alias+" instead of the systematic name "+name
+			out.write('\t'.join(tokens)+"\n")
+			importedCodes.add(alias)
+			
+	out.close()
+	
+	unimportedCodes = (usedCodes - importedCodes)
+	if len(unimportedCodes) > 0:
+		print "Missing metadata for: "
+		print unimportedCodes
+
+
+usedCodes = getUsedCodes('used-orfs.txt')
+
+metadataFileName='orf.txt'
+metadataFileNameOrg=metadataFileName+'.org'
+os.system("wget -O "+metadataFileNameOrg+" "+METADATA_FILE_URL);
+os.system("cat "+metadataFileNameOrg+" | cut -f1,3,4,5,6,7,16 > "+metadataFileName);
+metadataFile = open(metadataFileName)
+
+createUpdate(usedCodes, metadataFile, 'orf-update.txt')
+
+#os.remove(metadataFileNameOrg)
+os.remove(metadataFileName)