Merge pull request #1 from elijahspina/elijahspina-patch-1

Add files via upload

Author: flowscience

Python/ANISEED_ISHparse2.py

@@ -0,0 +1,79 @@
+#-------------------------------------------------------------------------------
+# Name:        module1
+# Purpose:
+#
+# Author:      Eli
+#
+# Created:     14/04/2015
+# Copyright:   (c) Eli 2015
+# Licence:     <your licence>
+#-------------------------------------------------------------------------------
+
+def main():
+    pass
+
+if __name__ == '__main__':
+    main()
+
+import sys
+
+#Read data
+f_in = open("C:/users/eli/downloads/ish/ish_ci.xml")
+
+#Print header row
+sys.stdout.write("gene" +"\t"+ "stage" +"\t"+ "tissue" +"\t"+ "pattern" +"\t"+ "original" +"\t"+ "source" +"\t"+ "exp" +"\t"+ "note" +'\n')
+
+#Set number of header rows to skip
+headers = 3
+count = 1
+source = False
+
+for line in f_in:
+
+    #Skip specified number of header lines
+    if count <= headers:
+        count+=1
+        pass
+
+    #Parse desired information
+    else:
+        if "experiment id" in line:
+            exp = "NA"
+            stage = "NA"
+            stage_source = "NA"
+            gene = "NA"
+            tissue = "NA"
+            note = "NA"
+            pattern = "NA"
+            original = "NA"
+            exp = line.split('"')[1]
+        if "developmental_stage" in line and source == False:
+            stage = line.split(">")[1].split('<')[0]
+            source = True
+
+        if "developmental_stage" in line and source == True:
+            stage_source = line.split(">")[1].split('<')[0]
+            source = False
+
+        if "probe_gene_predicted" in line:
+            gene = line.split(">")[1].split('<')[0]
+
+        if "staining_localization" in line:
+            tissue = line.split(">")[1].split('<')[0]
+
+        if "image_note" in line:
+            note = line.split(">")[1].split('<')[0]
+            if "Expression pattern:" in note:
+                pattern = note.split("Expression pattern:")[1].split("<")[0]
+
+            if "Original annotation:" in note:
+                original = note.split("Original annotation:")[1].split(".")[0]
+
+        else:
+            pass
+
+        #Output information for parsed record
+        if "/experiment" in line:
+            #results = [gene, stage, tissue, pattern, original, exp, note]
+            output = "\t".join([gene, stage, tissue, pattern, original, stage_source, exp, note])
+            sys.stdout.write(output + '\n')

Python/ANISEED_ISHparseET.py

@@ -0,0 +1,31 @@
+#-------------------------------------------------------------------------------
+# Name:        module2
+# Purpose:
+#
+# Author:      Eli
+#
+# Created:     14/04/2015
+# Copyright:   (c) Eli 2015
+# Licence:     <your licence>
+#-------------------------------------------------------------------------------
+
+def main():
+    pass
+
+if __name__ == '__main__':
+    main()
+
+#http://effbot.org/zone/element.htm
+
+import elementtree.ElementTree as ET
+import sys
+
+tree = ET.parse("C:/users/eli/downloads/ish/ish_ci.xml")
+
+# the tree root is the toplevel html element
+print tree.findtext("experiment")
+
+# if you need the root element, use getroot
+root = tree.getroot()
+
+print root