From e06e52134b151e4f12c8051a8c97656d8b2eb8b7 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 23 Nov 2010 12:59:08 +0000
Subject: [PATCH] LMS-1882 dynamix: script to update metadata from
yeastgenome.org
SVN: 18871
---
screening/source/python/dynamix-orf-update.py | 76 +
screening/source/python/used-orfs.txt | 4225 +++++++++++++++++
2 files changed, 4301 insertions(+)
create mode 100755 screening/source/python/dynamix-orf-update.py
create mode 100644 screening/source/python/used-orfs.txt
diff --git a/screening/source/python/dynamix-orf-update.py b/screening/source/python/dynamix-orf-update.py
new file mode 100755
index 00000000000..9889325acd3
--- /dev/null
+++ b/screening/source/python/dynamix-orf-update.py
@@ -0,0 +1,76 @@
+#!/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)
diff --git a/screening/source/python/used-orfs.txt b/screening/source/python/used-orfs.txt
new file mode 100644
index 00000000000..656be386751
--- /dev/null
+++ b/screening/source/python/used-orfs.txt
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--
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