Generate README (#35)

Generate README

Author: jjgao

AnnotatorCore.py

@@ -94,11 +94,10 @@ def getcuratedgenes(genelistfile):
 
 
 def getOncokbInfo():
-    ret = ['The data is generated on ' + date.today().strftime('%m/%d/%Y')]
+    ret = ['Files annotated on ' + date.today().strftime('%m/%d/%Y') + "\nOncoKB API URL: "+oncokbapiurl]
     try:
         info = json.load(urllib.urlopen(oncokbapiurl + "/info"))
-        ret.append('\n\nOncoKB data version: ' + info['dataVersion']['version'])
-        ret.append('\nThis version is released on ' + info['dataVersion']['date'])
+        ret.append('\nOncoKB data version: ' + info['dataVersion']['version']+', released on ' + info['dataVersion']['date'])
     except:
         print "error when fetch OncoKB info"
     return ''.join(ret)

GenarateReadMe.py

@@ -0,0 +1,42 @@
+#!/usr/bin/python
+
+import sys
+import getopt
+from AnnotatorCore import *
+
+def main(argv):
+
+    outputfile = ''
+
+    try:
+        opts, args = getopt.getopt(argv, "ho:u:")
+    except getopt.GetoptError:
+        print 'for help: python GenerateReadMe.py -h'
+        sys.exit(2)
+
+    for opt, arg in opts:
+        if opt == '-h':
+            print 'GenerateReadMe.py -o <output README file> [-u oncokb-base-url]'
+            print '  Default OncoKB base url is http://oncokb.org'
+            sys.exit()
+        elif opt in ("-o"):
+            outputfile = arg
+        elif opt in ("-u"):
+            setoncokbbaseurl(arg)
+
+    if outputfile=='':
+        print 'for help: python GenerateReadMe.py -h'
+        sys.exit(2)
+
+    generateReadme(outputfile)
+
+    print 'done!'
+
+if __name__ == "__main__":
+    # argv = [
+    #     '-o', 'data/README.txt'
+    # ]
+    # main(argv)
+
+    # print sys.argv[1:]
+    main(sys.argv[1:])

example.sh

@@ -8,8 +8,10 @@ OCNA="data/example_cna.oncokb.txt"
 IC="data/example_clinical.txt"
 OC="data/example_clinical.oncokb.txt"
 OCPDF="data/example_clinical.oncokb.pdf"
+README="data/example_README.txt"
 python MafAnnotator.py -i $IMAF -o $OMAF -c $IC
 python FusionAnnotator.py -i $IF -o $OF -c $IC
 python CnaAnnotator.py -i $ICNA -o $OCNA -c $IC
 python ClinicalDataAnnotator.py -i $IC -o $OC -a $OMAF,$OCNA,$OF
 python OncoKBPlots.py -i $OC -o $OCPDF -c ONCOTREE_CODE #-n 10
+python GenarateReadMe.py -o $README