# HG changeset patch
# User peterjc
# Date 1343667414 14400
# Node ID 976a5f2833cd7c5d3dc840617124fbc1cccd5d2b
# Parent  9b45a87431005c7fdf28a2077bd6ed5df55ef75e
Uploaded v0.1.1 of the bundle, which fixes an error in the header of the tabular output produced for Promoter 2.0

diff -r 9b45a8743100 -r 976a5f2833cd tools/protein_analysis/README
--- a/tools/protein_analysis/README	Mon Jul 30 10:25:07 2012 -0400
+++ b/tools/protein_analysis/README	Mon Jul 30 12:56:54 2012 -0400
@@ -126,6 +126,7 @@
 v0.0.9 - Added our RXLR motifs tool to the suite.
 v0.1.0 - Added Promoter 2.0 wrapper (similar to SignalP & TMHMM wrappers)
        - Support Galaxy's <parallelism> tag for SignalP, TMHMM & Promoter
+v0.1.1 - Fixed an error in the header of the tabular output from Promoter
 
 Developers
 ==========
diff -r 9b45a8743100 -r 976a5f2833cd tools/protein_analysis/promoter2.py
--- a/tools/protein_analysis/promoter2.py	Mon Jul 30 10:25:07 2012 -0400
+++ b/tools/protein_analysis/promoter2.py	Mon Jul 30 12:56:54 2012 -0400
@@ -73,7 +73,6 @@
     """Parse text output into tabular, return query count."""
     identifier = None
     queries = 0
-    #out.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n")
     for line in raw_handle:
         #print repr(line)
         if not line.strip() or line == "Promoter prediction:\n":
@@ -99,7 +98,6 @@
                                   "Highly likely prediction"]:
                 stop_err("ERROR: Problem with line: %r" % line)
             out_handle.write("%s\t%s\t%s\t%s\n" % (identifier, position, score, likelihood))
-    #out.close()
     return queries
     
 working_dir, bin = get_path_and_binary()
@@ -147,7 +145,7 @@
 del jobs
 
 out_handle = open(tabular_file, "w")
-out_handle.write("#Identifier\tDescription\tPosition\tScore\tLikelihood\n")
+out_handle.write("#Identifier\tPosition\tScore\tLikelihood\n")
 queries = 0
 for temp in temp_files:
     data_handle = open(temp)
diff -r 9b45a8743100 -r 976a5f2833cd tools/protein_analysis/promoter2.xml
--- a/tools/protein_analysis/promoter2.xml	Mon Jul 30 10:25:07 2012 -0400
+++ b/tools/protein_analysis/promoter2.xml	Mon Jul 30 12:56:54 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.1">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.2">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
@@ -22,7 +22,7 @@
     
 **What it does**
 
-This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoters sequences using a Neural Network (NN) model.
+This calls the Promoter 2.0 tool for prediction of eukaryotic PolII promoter sequences using a Neural Network (NN) model.
 
 The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):