# HG changeset patch
# User davidmurphy
# Date 1327929477 18000
# Node ID f3462128e87ca313d63f1e7ffcccb4dbd24c817a
# Parent  5149eb3a89c2e75b747fa978c94674296c26907a
Minor alterations to the galaxy interface with some better examples and error messages added.

diff -r 5149eb3a89c2 -r f3462128e87c Codonlogo.xml
--- a/Codonlogo.xml	Fri Jan 20 09:03:40 2012 -0500
+++ b/Codonlogo.xml	Mon Jan 30 08:17:57 2012 -0500
@@ -1,6 +1,6 @@
 <tool id="codonlogo" name="Codon Logo" version="3">
   <description>generator for fasta (eg Clustal alignments)</description>
-  <command interpreter="/usr/tmp/bin/python2.7 -W ignore::DeprecationWarning"> 
+  <command interpreter="python -W ignore::DeprecationWarning"> 
     codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks -X $showxaxis --show-yaxis $showyaxis --errorbars $errorbars -G $strict --fineprint "$fineprint" --stack-width $stackwidth --stack-height $stackheight --box $box --resolution $resolution --scale-width $scalewidth
 
     #if str($ylabel) != ''
@@ -24,13 +24,13 @@
     -R $compfile 
     #end if
     #if str($comp.mode) == 'Escherichiacoli'
-    -R Escherichiacoli.txt
+    --comp escherichiacoli
     #end if
     #if str($comp.mode) == 'Saccharomycescerevisiae'
-    -R Saccharomycescerevisiae.txt
+    --comp saccharomycescerevisiae
     #end if
     #if str($comp.mode) == 'Homosapiens'
-    -R Homosapiens.txt
+    --comp homosapiens
     #end if
     
     #if $colours.colour == 'part'
@@ -404,13 +404,12 @@
     </conditional>
     <conditional name="comp">
       <param name="mode" type="select" label="Select expected composition: 'equiprobable', 'none' (no small sample correction), or supply a file">
-        
-        <option value="equiprobable" >equiprobable</option>
-        <option value="none" >none</option>
-<!--	<option value="Escherichiacoli" >Escherichiacoli</option>
-	<option value="Homosapiens" >Homosapiens</option>
-	<option value="Saccharomycescerevisiae" >Saccharomycescerevisiae</option>-->
-        <option value="file">from file</option>
+        <option value="none" >No small sample correction</option>       
+        <option value="equiprobable" >Equiprobable</option>
+        <option value="Homosapiens" >Human</option>
+        <option value="Yeast" >Saccharomycescerevisiae</option>
+        <option value="E.Coli" >Escherichiacoli</option>
+        <option value="From File">from file</option>
         
       </param>
       <when value="auto">
diff -r 5149eb3a89c2 -r f3462128e87c LICENSE.txt
diff -r 5149eb3a89c2 -r f3462128e87c PKG-INFO
diff -r 5149eb3a89c2 -r f3462128e87c README.txt
--- a/README.txt	Fri Jan 20 09:03:40 2012 -0500
+++ b/README.txt	Mon Jan 30 08:17:57 2012 -0500
@@ -1,51 +1,47 @@
-
-CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 
-logos from biological sequence alignments.  It can be run from the command line as a standalone webserver or as a CGI webapp.
-
-
-For help on the command line interface run
-    ./codonlogo --help
-
-To build a simple logo run
-    ./codonlogo  < cap.fa > logo.eps
-
-
-To run as a standalone webserver at localhost:8080 
-    ./codonlogo --server
-
-
-An example file of probabilities is included, examplepriorfile.txt
-It can be used with the following command.
-
-    ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps
-
-
-examplepriorfile contains the frequencies for codons in human CDS regions. 
-
-
-KNOWN ISSUES:
-
-There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault or prevent codonlogos from being generated in anything other than eps format. 
-
-This is believed to be an issue with ghostscript and a bug report has been submitted to the ghostscript mailing list.
-This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 of ghostscript or earlier .
-
-
-
-For converting files to a suitable format the following sites can be used:
-
+
+CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 
+logos from biological sequence alignments.  It can be run on the command line,
+as a standalone webserver or as a CGI webapp.
+
+
+For help on the command line interface run
+    ./codonlogo --help
+
+To build a simple logo run
+    ./codonlogo  < cap.fa > logo.eps
+
+
+To run as a standalone webserver at localhost:8080 
+    ./codonlogo --server
+
+
+An example file of probabilities is included, examplepriorfile.txt
+It can be used with the following command.
+
+    ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
+
+
+examplepriorfile contains the frequencies for codons in human CDS regions. 
+
+
+There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. 
+This is not believed to be a problem with CodonLogo.
+This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
+
+For converting files to a suitable format the following sites can be used:
+
 http://genome.nci.nih.gov/tools/reformat.html
 http://www-bimas.cit.nih.gov/molbio/readseq/
-
-
-
-
--- Distribution and Modification --
-This package is distributed under the new BSD Open Source License. 
-Please see the LICENSE.txt file for details on copyright and licensing.
-The CodonLogo source code can be downloaded from 
-http://recode.ucc.ie/CodonLogo
-
-CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
-computational biology (http://code.google.com/p/corebio), and the python
-array package 'numpy' (http://www.scipy.org/Download)
+
+
+
+
+-- Distribution and Modification --
+This package is distributed under the new BSD Open Source License. 
+Please see the LICENSE.txt file for details on copyright and licensing.
+The CodonLogo source code can be downloaded from 
+http://recode.ucc.ie/CodonLogo
+
+CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
+computational biology (http://code.google.com/p/corebio), and the python
+array package 'numpy' (http://www.scipy.org/Download)
diff -r 5149eb3a89c2 -r f3462128e87c README.txt~
--- a/README.txt~	Fri Jan 20 09:03:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,47 +0,0 @@
-
-CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 
-logos from biological sequence alignments.  It can be run on the command line,
-as a standalone webserver or as a CGI webapp.
-
-
-For help on the command line interface run
-    ./codonlogo --help
-
-To build a simple logo run
-    ./codonlogo  < cap.fa > logo.eps
-
-
-To run as a standalone webserver at localhost:8080 
-    ./codonlogo --server
-
-
-An example file of probabilities is included, examplepriorfile.txt
-It can be used with the following command.
-
-    ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
-
-
-examplepriorfile contains the frequencies for codons in human CDS regions. 
-
-
-There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. 
-This is not believed to be a problem with CodonLogo.
-This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
-
-For converting files to a suitable format the following sites can be used:
-
-http://genome.nci.nih.gov/tools/reformat.html
-http://www-bimas.cit.nih.gov/molbio/readseq/
-
-
-
-
--- Distribution and Modification --
-This package is distributed under the new BSD Open Source License. 
-Please see the LICENSE.txt file for details on copyright and licensing.
-The CodonLogo source code can be downloaded from 
-http://recode.ucc.ie/CodonLogo
-
-CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
-computational biology (http://code.google.com/p/corebio), and the python
-array package 'numpy' (http://www.scipy.org/Download)
diff -r 5149eb3a89c2 -r f3462128e87c build_test.sh
diff -r 5149eb3a89c2 -r f3462128e87c cap.fa
diff -r 5149eb3a89c2 -r f3462128e87c capu.fa
diff -r 5149eb3a89c2 -r f3462128e87c codonlogo
diff -r 5149eb3a89c2 -r f3462128e87c corebio/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/_future/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/_future/_string.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/_future/subprocess.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/_version.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/data.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/data/blosum62.mat
diff -r 5149eb3a89c2 -r f3462128e87c corebio/data/blosum80.mat
diff -r 5149eb3a89c2 -r f3462128e87c corebio/data/pam120.mat
diff -r 5149eb3a89c2 -r f3462128e87c corebio/data/pam250.mat
diff -r 5149eb3a89c2 -r f3462128e87c corebio/moremath.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/resource/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/resource/astral.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/resource/scop.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/resource/stride.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/_nexus/Nodes.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/_nexus/Trees.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/_nexus/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/array_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/clustal_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/fasta_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/genbank_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/intelligenetics_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/msf_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/nbrf_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/nexus_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/null_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/phylip_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/plain_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/stockholm_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/seq_io/table_io.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/ssearch_io/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/ssearch_io/blastxml.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/ssearch_io/fasta.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/transform.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/utils/__init__.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/utils/_which.py
diff -r 5149eb3a89c2 -r f3462128e87c corebio/utils/deoptparse.py
diff -r 5149eb3a89c2 -r f3462128e87c examples/0_Frame_output.pdf
Binary file examples/0_Frame_output.pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c examples/1_Frame_output.pdf
Binary file examples/1_Frame_output.pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c examples/2_Frame_output.pdf
Binary file examples/2_Frame_output.pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c examples/Galaxy-Workflow-Figure(1).ga
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/examples/Galaxy-Workflow-Figure(1).ga	Mon Jan 30 08:17:57 2012 -0500
@@ -0,0 +1,118 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "Generates part B", 
+    "format-version": "0.1", 
+    "name": "Figure", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 197, 
+                "top": 384
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Codon Logo", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 580, 
+                "top": 228
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "codonlogo", 
+            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"0\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"0 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
+            "tool_version": "3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Codon Logo", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 580, 
+                "top": 360
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "codonlogo", 
+            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"1\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+1 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
+            "tool_version": "3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Codon Logo", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "pdf"
+                }
+            ], 
+            "position": {
+                "left": 580, 
+                "top": 493
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "codonlogo", 
+            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"2\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+2 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
+            "tool_version": "3", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
diff -r 5149eb3a89c2 -r f3462128e87c examples/Galaxy-Workflow-Figure.ga
--- a/examples/Galaxy-Workflow-Figure.ga	Fri Jan 20 09:03:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,118 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "Generates part B", 
-    "format-version": "0.1", 
-    "name": "Figure", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 197, 
-                "top": 384
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {
-                "input": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Codon Logo", 
-            "outputs": [
-                {
-                    "name": "output", 
-                    "type": "pdf"
-                }
-            ], 
-            "position": {
-                "left": 580, 
-                "top": 228
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "codonlogo", 
-            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"0\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"0 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
-            "tool_version": "3", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "input": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Codon Logo", 
-            "outputs": [
-                {
-                    "name": "output", 
-                    "type": "pdf"
-                }
-            ], 
-            "position": {
-                "left": 580, 
-                "top": 360
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "codonlogo", 
-            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"1\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+1 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
-            "tool_version": "3", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {
-                "input": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Codon Logo", 
-            "outputs": [
-                {
-                    "name": "output", 
-                    "type": "pdf"
-                }
-            ], 
-            "position": {
-                "left": 580, 
-                "top": 493
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "codonlogo", 
-            "tool_state": "{\"outformat\": \"\\\"pdf\\\"\", \"frame\": \"\\\"2\\\"\", \"size\": \"\\\"large\\\"\", \"__page__\": 0, \"colours\": \"{\\\"colour\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"strict\": \"\\\"False\\\"\", \"logoname\": \"\\\"+2 Frame\\\"\", \"ylabel\": \"\\\"\\\"\", \"input\": \"null\", \"stackheight\": \"\\\"100\\\"\", \"scalewidth\": \"\\\"True\\\"\", \"showyaxis\": \"\\\"True\\\"\", \"comp\": \"{\\\"mode\\\": \\\"equiprobable\\\", \\\"__current_case__\\\": 1}\", \"showxaxis\": \"\\\"True\\\"\", \"stackwidth\": \"\\\"40.0\\\"\", \"box\": \"\\\"False\\\"\", \"fineprint\": \"\\\"\\\"\", \"range\": \"{\\\"seqend\\\": \\\"16\\\", \\\"mode\\\": \\\"part\\\", \\\"__current_case__\\\": 1, \\\"seqstart\\\": \\\"6\\\"}\", \"xlabel\": \"\\\"\\\"\", \"errorbars\": \"\\\"True\\\"\", \"resolution\": \"\\\"96\\\"\", \"stacks\": \"\\\"20\\\"\"}", 
-            "tool_version": "3", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
diff -r 5149eb3a89c2 -r f3462128e87c examples/Galaxy53-[_2_Frame_output.pdf](1).pdf
Binary file examples/Galaxy53-[_2_Frame_output.pdf](1).pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c examples/Galaxy54-[_1_Frame_output.pdf].pdf
Binary file examples/Galaxy54-[_1_Frame_output.pdf].pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c examples/Galaxy55-[0_Frame_output.pdf].pdf
Binary file examples/Galaxy55-[0_Frame_output.pdf].pdf has changed
diff -r 5149eb3a89c2 -r f3462128e87c inter.py
diff -r 5149eb3a89c2 -r f3462128e87c setup.py
diff -r 5149eb3a89c2 -r f3462128e87c test_weblogo.py
diff -r 5149eb3a89c2 -r f3462128e87c tests/data/Rv3829c.fasta
diff -r 5149eb3a89c2 -r f3462128e87c tests/data/cap.fa
diff -r 5149eb3a89c2 -r f3462128e87c tests/data/capu.fa
diff -r 5149eb3a89c2 -r f3462128e87c tests/data/cox2.msf
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/.__init__.py.kate-swp
Binary file weblogolib/.__init__.py.kate-swp has changed
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/Escherichiacoli.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weblogolib/Escherichiacoli.txt	Mon Jan 30 08:17:57 2012 -0500
@@ -0,0 +1,64 @@
+UUU	19.7
+UUC	15
+UUA	15.2
+UUG	11.9
+CUU	11.9
+CUC	10.5
+CUA	5.3
+CUG	46.9
+AUU	30.5
+AUC	18.2
+AUA	3.7
+AUG	24.8
+GUU	16.8
+GUC	11.7
+GUA	11.5
+GUG	26.4
+UCU	5.7
+UCC	5.5
+UCA	7.8
+UCG	8
+CCU	8.4
+CCC	6.4
+CCA	6.6
+CCG	26.7
+ACU	8
+ACC	22.8
+ACA	6.4
+ACG	11.5
+GCU	10.7
+GCC	31.6
+GCA	21.1
+GCG	38.5
+UAU	16.8
+UAC	14.6
+UAA	1.8
+UAG	0
+CAU	15.8
+CAC	13.1
+CAA	12.1
+CAG	27.7
+AAU	21.9
+AAC	24.4
+AAA	33.2
+AAG	12.1
+GAU	37.9
+GAC	20.5
+GAA	43.7
+GAG	18.4
+UGU	5.9
+UGC	8
+UGA	1
+UGG	10.7
+CGU	21.1
+CGC	26
+CGA	4.3
+CGG	4.1
+AGU	7.2
+AGC	16.6
+AGA	1.4
+AGG	1.6
+GGU	21.3
+GGC	33.4
+GGA	9.2
+GGG	8.6
\ No newline at end of file
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/Homosapiens.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weblogolib/Homosapiens.txt	Mon Jan 30 08:17:57 2012 -0500
@@ -0,0 +1,64 @@
+UUU	17.6
+UUC	20.3
+UUA	7.7
+UUG	12.9
+CUU	13.2
+CUC	19.6
+CUA	7.2
+CUG	39.6
+AUU	16
+AUC	20.8
+AUA	7.5
+AUG	22
+GUU	11
+GUC	14.5
+GUA	7.1
+GUG	28.1
+UCU	15.2
+UCC	17.7
+UCA	12.2
+UCG	4.4
+CCU	17.5
+CCC	19.8
+CCA	16.9
+CCG	6.9
+ACU	13.1
+ACC	18.9
+ACA	15.1
+ACG	6.1
+GCU	18.4
+GCC	27.7
+GCA	15.8
+GCG	7.4
+UAU	12.2
+UAC	15.3
+UAA	1
+UAG	0.8
+CAU	10.9
+CAC	15.1
+CAA	12.3
+CAG	34.2
+AAU	17
+AAC	19.1
+AAA	24.4
+AAG	31.9
+GAU	21.8
+GAC	25.1
+GAA	29
+GAG	39.6
+UGU	10.6
+UGC	12.6
+UGA	1.6
+UGG	13.2
+CGU	4.5
+CGC	10.4
+CGA	6.2
+CGG	11.4
+AGU	12.1
+AGC	19.5
+AGA	12.2
+AGG	12
+GGU	10.8
+GGC	22.2
+GGA	16.5
+GGG	16.5
\ No newline at end of file
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/Saccharomycescerevisiae.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/weblogolib/Saccharomycescerevisiae.txt	Mon Jan 30 08:17:57 2012 -0500
@@ -0,0 +1,64 @@
+UUU	26.1
+UUC	18.4
+UUA	26.2
+UUG	27.2
+CUU	12.3
+CUC	5.4
+CUA	13.4
+CUG	10.5
+AUU	30.1
+AUC	17.2
+AUA	17.8
+AUG	20.9
+GUU	22.1
+GUC	11.8
+GUA	11.8
+GUG	10.8
+UCU	23.5
+UCC	14.2
+UCA	18.7
+UCG	8.6
+CCU	13.5
+CCC	6.8
+CCA	18.3
+CCG	5.3
+ACU	20.3
+ACC	12.7
+ACA	17.8
+ACG	8
+GCU	21.2
+GCC	12.6
+GCA	16.2
+GCG	6.2
+UAU	18.8
+UAC	14.8
+UAA	1.1
+UAG	0.5
+CAU	13.6
+CAC	7.8
+CAA	27.3
+CAG	12.1
+AAU	35.7
+AAC	24.8
+AAA	41.9
+AAG	30.8
+GAU	37.6
+GAC	20.2
+GAA	45.6
+GAG	19.2
+UGU	8.1
+UGC	4.8
+UGA	0.7
+UGG	10.4
+CGU	6.4
+CGC	2.6
+CGA	3
+CGG	1.7
+AGU	14.2
+AGC	9.8
+AGA	21.3
+AGG	9.2
+GGU	23.9
+GGC	9.8
+GGA	10.9
+GGG	6
\ No newline at end of file
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/__init__.py
--- a/weblogolib/__init__.py	Fri Jan 20 09:03:40 2012 -0500
+++ b/weblogolib/__init__.py	Mon Jan 30 08:17:57 2012 -0500
@@ -982,7 +982,12 @@
     if comp.lower() == 'equiprobable' :
         prior = weight * equiprobable_distribution(len(alphabet)) 
         
-        
+    elif comp.lower() == 'escherichiacoli' :
+	composition="{'CTT': 0.7616, 'ATG': 1.5872, 'ACA': 0.4096, 'ACG': 0.736, 'ATC': 1.1648, 'AAC': 1.5615999999999999, 'ATA': 0.2368, 'AGG': 0.1024, 'CCT': 0.5376000000000001, 'ACT': 0.512, 'AGC': 1.0624, 'AAG': 0.7744, 'AGA': 0.0896, 'CAT': 1.0112, 'AAT': 1.4016, 'ATT': 1.952, 'CTG': 3.0016, 'CTA': 0.3392, 'CTC': 0.672, 'CAC': 0.8383999999999999, 'AAA': 2.1248, 'CCG': 1.7087999999999999, 'AGT': 0.4608, 'CCA': 0.4224, 'CAA': 0.7744, 'CCC': 0.4096, 'TAT': 1.0752000000000002, 'GGT': 1.3632, 'TGT': 0.37760000000000005, 'CGA': 0.2752, 'CAG': 1.7728, 'TCT': 0.3648, 'GAT': 2.4255999999999998, 'CGG': 0.26239999999999997, 'TTT': 1.2608, 'TGC': 0.512, 'GGG': 0.5504, 'TAG': 1e-06, 'GGA': 0.5888, 'TAA': 0.1152, 'GGC': 2.1376, 'TAC': 0.9344, 'TTC': 0.96, 'TCG': 0.512, 'TTA': 0.9728, 'TTG': 0.7616, 'TCC': 0.352, 'ACC': 1.4592, 'TCA': 0.4992, 'GCA': 1.3504, 'GTA': 0.736, 'GCC': 2.0224, 'GTC': 0.7487999999999999, 'GCG': 2.464, 'GTG': 1.6896, 'GAG': 1.1776, 'GTT': 1.0752000000000002, 'GCT': 0.6848, 'TGA': 0.064, 'GAC': 1.312, 'CGT': 1.3504, 'TGG': 0.6848, 'GAA': 2.7968, 'CGC': 1.664}"
+    elif comp.lower() == 'homosapiens' :
+	composition="{'CTT': 0.8448, 'ATG': 1.408, 'ACA': 0.9663999999999999, 'ACG': 0.39039999999999997, 'ATC': 1.3312, 'AAC': 1.2224000000000002, 'ATA': 0.48, 'AGG': 0.768, 'CCT': 1.12, 'ACT': 0.8383999999999999, 'AGC': 1.248, 'AAG': 2.0416, 'AGA': 0.7807999999999999, 'CAT': 0.6976, 'AAT': 1.088, 'ATT': 1.024, 'CTG': 2.5344, 'CTA': 0.4608, 'CTC': 1.2544000000000002, 'CAC': 0.9663999999999999, 'AAA': 1.5615999999999999, 'CCG': 0.44160000000000005, 'AGT': 0.7744, 'CCA': 1.0816, 'CAA': 0.7872, 'CCC': 1.2672, 'TAT': 0.7807999999999999, 'GGT': 0.6912, 'TGT': 0.6784, 'CGA': 0.3968, 'CAG': 2.1888, 'TCT': 0.9728, 'GAT': 1.3952, 'CGG': 0.7296, 'TTT': 1.1264, 'TGC': 0.8064, 'GGG': 1.056, 'TAG': 0.0512, 'GGA': 1.056, 'TAA': 0.064, 'GGC': 1.4208, 'TAC': 0.9792000000000001, 'TTC': 1.2992000000000001, 'TCG': 0.2816, 'TTA': 0.4928, 'TTG': 0.8256, 'TCC': 1.1328, 'ACC': 1.2096, 'TCA': 0.7807999999999999, 'GCA': 1.0112, 'GTA': 0.45439999999999997, 'GCC': 1.7728, 'GTC': 0.928, 'GCG': 0.4736, 'GTG': 1.7984, 'GAG': 2.5344, 'GTT': 0.704, 'GCT': 1.1776, 'TGA': 0.1024, 'GAC': 1.6064, 'CGT': 0.288, 'TGG': 0.8448, 'GAA': 1.856, 'CGC': 0.6656}"
+    elif comp.lower() == 'saccharomycescerevisiae' :
+	composition="{'CTT': 0.7872, 'ATG': 1.3376, 'ACA': 1.1392, 'ACG': 0.512, 'ATC': 1.1008, 'AAC': 1.5872, 'ATA': 1.1392, 'AGG': 0.5888, 'CCT': 0.864, 'ACT': 1.2992000000000001, 'AGC': 0.6272000000000001, 'AAG': 1.9712, 'AGA': 1.3632, 'CAT': 0.8704, 'AAT': 2.2848, 'ATT': 1.9264000000000001, 'CTG': 0.672, 'CTA': 0.8576, 'CTC': 0.3456, 'CAC': 0.4992, 'AAA': 2.6816, 'CCG': 0.3392, 'AGT': 0.9087999999999999, 'CCA': 1.1712, 'CAA': 1.7472, 'CCC': 0.4352, 'TAT': 1.2032, 'GGT': 1.5295999999999998, 'TGT': 0.5184, 'CGA': 0.192, 'CAG': 0.7744, 'TCT': 1.504, 'GAT': 2.4064, 'CGG': 0.1088, 'TTT': 1.6704, 'TGC': 0.3072, 'GGG': 0.384, 'TAG': 0.032, 'GGA': 0.6976, 'TAA': 0.0704, 'GGC': 0.6272000000000001, 'TAC': 0.9472, 'TTC': 1.1776, 'TCG': 0.5504, 'TTA': 1.6767999999999998, 'TTG': 1.7408, 'TCC': 0.9087999999999999, 'ACC': 0.8128, 'TCA': 1.1967999999999999, 'GCA': 1.0368, 'GTA': 0.7552000000000001, 'GCC': 0.8064, 'GTC': 0.7552000000000001, 'GCG': 0.3968, 'GTG': 0.6912, 'GAG': 1.2288, 'GTT': 1.4144, 'GCT': 1.3568, 'TGA': 0.0448, 'GAC': 1.2928, 'CGT': 0.4096, 'TGG': 0.6656, 'GAA': 2.9184, 'CGC': 0.1664}"
     elif comp.lower() == 'auto' or comp.lower() == 'automatic':
         if alphabet == unambiguous_protein_alphabet :
             prior =  weight * asarray(aa_composition, float64)
@@ -1256,7 +1261,7 @@
 		if len(seqs[i][(counter):(counter+3)].strip("GATUC"))==1 or len(seqs[i][(counter):(counter+3)].strip("GATUC"))==2 :
 		  print >>sys.stderr, 'Warning:Incomplete or non GATUC codon detected:', seqs[i][(counter):(counter+3)]
 		  print >>sys.stderr, 'Position:',counter
-		  print >>sys.stderr, 'Sequence:',i
+		  print >>sys.stderr, 'Sequence:',(i+1)
 		  print >>sys.stderr, 'This will be treated as ---'
 
 
@@ -1386,7 +1391,8 @@
 	priordict[line[0].upper().replace("U", "T")]=(float(line[1])/1000)*64
       else:
 	priordict[line[0].upper().replace("T", "U")]=(float(line[1])/1000)*64
-
+      if priordict[line[0].upper().replace("U", "T")] == 0:
+	priordict[line[0].upper().replace("U", "T")] = 0.000001
     return priordict
 
 def _build_logodata(options) :
@@ -1632,7 +1638,7 @@
         action="store",
         type="string",
         default = "auto",
-        help="The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (Do not perform any compositional adjustment), ",
+        help="The expected composition of the sequences: 'auto' (default), 'equiprobable', 'none' (Do not perform any compositional adjustment), or 'escherichiacoli'  'homosapiens'  'saccharomycescerevisiae' for ecoli, human and SC codon frequencies.",
         metavar="COMP.")
 
     data_grp.add_option( "", "--weight",
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/_cgi.py
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/color.py
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/colorscheme.py
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/create.cgi
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/create_html_template.html
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/examples.html
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/index.html
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/logo.css
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/manual.html
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/htdocs/test.html
diff -r 5149eb3a89c2 -r f3462128e87c weblogolib/template.eps