added script to add metadata to picrust precalc file

add_picrust_metadata.py

@@ -0,0 +1,67 @@
+#!/usr/bin/python 
+
+import sys
+import argparse
+
+parser = argparse.ArgumentParser(
+                        description="Basic script to output function metadata "
+                                    "in same order as predicted table. "
+                                    "Metadata file should contain 1 function "
+                                    "per line.",
+                                    epilog="Usage example:\n"
+                                    "add_picrust_metadata.py -i "
+                                    "predicted.tab -m metadata.txt"
+                                    "-o metadata_out.txt",
+                        formatter_class=argparse.RawDescriptionHelpFormatter)
+
+parser.add_argument("-i", "--input", help="Predicted trait table.", 
+                    required=True, type=str)
+
+parser.add_argument("-m", "--meta", help="File containing metadata.", 
+                    required=True, type=str)
+
+parser.add_argument("-o", "--output", help="Output metadata line to concatenate.", 
+                    required=True, type=str)
+
+args = parser.parse_args()
+
+count_file = args.input
+metadata_file = args.meta
+new_file = args.output
+
+out_fh=open(new_file,'w')
+
+def load_metadata(metadata_file_name):
+
+    metadata={}
+    metadata_fh=open(metadata_file_name)
+    meta_name=metadata_fh.readline().strip().split('\t')[1]
+    for line in metadata_fh:
+        meta_fields=line.strip().split('\t')
+        if len(meta_fields)> 1:
+            metadata[meta_fields[0]]=meta_fields[1]
+    return metadata,meta_name
+
+
+count_fh=open(count_file)
+header=count_fh.readline()
+fields=header.strip().split('\t')
+fields=fields[1:-1]
+
+metadata,meta_name=load_metadata(metadata_file)
+
+meta_line=[meta_name]
+for field in fields:
+    if field in metadata:
+        if metadata[field] =='':
+            meta_line.append('None')
+        else:
+            meta_line.append(metadata[field])
+
+    else:
+        print "Couldn't find metadata for "+field
+        meta_line.append('None')
+
+meta_line_str = "\t".join(meta_line)+"\n"
+out_fh.write(meta_line_str)
+