Galaxy |

Changeset 0:baf7031d470e (2011-06-07)

Next changeset 1:f1323a651777 (2013-05-06)

Commit message:
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository

added:
tools/plotting/venn_list.py
tools/plotting/venn_list.txt
tools/plotting/venn_list.xml

diff -r 000000000000 -r baf7031d470e tools/plotting/venn_list.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/venn_list.py Tue Jun 07 18:08:11 2011 -0400

[

@@ -0,0 +1,135 @@
+#!/usr/bin/env python
+"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
+
+This script is copyright 2010 by Peter Cock, The James Hutton Institute
+(formerly SCRI), UK. All rights reserved.
+See accompanying text file for licence details (MIT/BSD style).
+
+This is version 0.0.3 of the script.
+"""
+
+
+import sys
+import rpy
+
+def stop_err(msg, error_level=1):
+    """Print error message to stdout and quit with given error level."""
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(error_level)
+
+try:
+    import rpy
+except ImportError:
+    stop_err("Requires the Python library rpy (to call R)")
+
+try:
+    rpy.r.library("limma")
+except:
+    stop_err("Requires the R library limma (for vennDiagram function)")
+
+
+if len(sys.argv)-1 not in [7, 10, 13]:
+    stop_err("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv)-1))
+
+all_file, all_type, all_label = sys.argv[1:4]
+set_data = []
+if len(sys.argv)-1 >= 7:
+    set_data.append(tuple(sys.argv[4:7]))
+if len(sys.argv)-1 >= 10:
+    set_data.append(tuple(sys.argv[7:10]))
+if len(sys.argv)-1 >= 13:
+    set_data.append(tuple(sys.argv[10:13]))
+pdf_file = sys.argv[-1]
+n = len(set_data)
+print "Doing %i-way Venn Diagram" % n
+
+def load_ids(filename, filetype):
+    if filetype=="tabular":
+        for line in open(filename):
+            if not line.startswith("#"):
+                yield line.rstrip("\n").split("\t",1)[0]
+    elif filetype=="fasta":
+        for line in open(filename):
+            if line.startswith(">"):
+                yield line[1:].rstrip("\n").split(None,1)[0]
+    elif filetype.startswith("fastq"):
+        #Use the Galaxy library not Biopython to cope with CS
+        from galaxy_utils.sequence.fastq import fastqReader
+        handle = open(filename, "rU")
+        for record in fastqReader(handle):
+            #The [1:] is because the fastaReader leaves the @ on the identifer.
+            yield record.identifier.split()[0][1:]
+        handle.close()
+    elif filetype=="sff":
+        try:
+            from Bio.SeqIO import index
+        except ImportError:
+            stop_err("Require Biopython 1.54 or later (to read SFF files)")
+        #This will read the SFF index block if present (very fast)
+        for name in index(filename, "sff"):
+            yield name
+    else:
+        stop_err("Unexpected file type %s" % filetype)
+
+def load_ids_whitelist(filename, filetype, whitelist):
+    for name in load_ids(filename, filetype):
+        if name in whitelist:
+            yield name
+        else:
+            stop_err("Unexpected ID %s in %s file %s" % (name, filetype, filename))
+
+if all_file in ["", "-", '""', '"-"']:
+    #Load without white list
+    sets = [set(load_ids(f,t)) for (f,t,c) in set_data]
+    #Take union
+    all = set()
+    for s in sets:
+        all.update(s)
+    print "Inferred total of %i IDs" % len(all)
+else:
+    all = set(load_ids(all_file, all_type))
+    print "Total of %i IDs" % len(all)
+    sets = [set(load_ids_whitelist(f,t,all)) for (f,t,c) in set_data]
+
+for s, (f,t,c) in zip(sets, set_data):
+    print "%i in %s" % (len(s), c)
+
+#Now call R library to draw simple Venn diagram
+try:
+    #Create dummy Venn diagram counts object for three groups
+    cols = 'c("%s")' % '","'.join("Set%i" % (i+1) for i in range(n))
+    rpy.r('groups <- cbind(%s)' % ','.join(['1']*n))
+    rpy.r('colnames(groups) <- %s' % cols)
+    rpy.r('vc <- vennCounts(groups)')
+    #Populate the 2^n classes with real counts
+    #Don't make any assumptions about the class order
+    #print rpy.r('vc')
+    for index, row in enumerate(rpy.r('vc[,%s]' % cols)):
+        if isinstance(row, int) or isinstance(row, float):
+            #Hack for rpy being too clever for single element row
+            row = [row]
+        names = all
+        for wanted, s in zip(row, sets):
+            if wanted:
+                names = names.intersection(s)
+            else:
+                names = names.difference(s)
+        rpy.r('vc[%i,"Counts"] <- %i' % (index+1, len(names)))
+    #print rpy.r('vc')
+    if n == 1:
+        #Single circle, don't need to add (Total XXX) line
+        names = [c for (t,f,c) in set_data]
+    else:
+        names = ["%s\n(Total %i)" % (c, len(s)) for s, (f,t,c) in zip(sets, set_data)]
+    rpy.r.assign("names", names)
+    rpy.r.assign("colors", ["red","green","blue"][:n])
+    rpy.r.pdf(pdf_file, 8, 8)
+    rpy.r("""vennDiagram(vc, include="both", names=names,
+                         main="%s", sub="(Total %i)",
+                         circle.col=colors)
+                         """ % (all_label, len(all)))
+    rpy.r.dev_off()
+except Exception, exc:
+    stop_err( "%s" %str( exc ) )
+rpy.r.quit( save="no" )
+print "Done"

diff -r 000000000000 -r baf7031d470e tools/plotting/venn_list.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/venn_list.txt Tue Jun 07 18:08:11 2011 -0400

@@ -0,0 +1,75 @@
+Galaxy tool to draw a Venn Diagram with up to 3 sets
+====================================================
+
+This tool is copyright 2011 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (using both the Galaxy and Biopython library
+functions) to extract ID lists from tabular, FASTA, FASTQ or SFF files to build
+sets, which are then drawn using the R limma package function vennDiagram
+(called from Python using rpy).
+
+There are just two files to install:
+
+* venn_list.py (the Python script)
+* venn_list.xml (the Galaxy tool definition)
+
+The suggested location is in the Galaxy folder tools/plotting next to other
+graph drawing tools.
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. The suggested location is in the "Graph/Display Data" section. Simply add
+the line:
+
+<tool file="plotting/venn_list.xml" />
+
+You will also need to install Biopython 1.54 or later, and the R/Bioconductor
+pacakge limma. You should already have rpy installed for other Galaxy tools.
+
+
+History
+=======
+
+v0.0.3 - Initial public release.
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+tar -czf venn_list.tar.gz tools/plotting/venn_list.*
+
+Check this worked:
+
+$ tar -tzf venn_list.tar.gz
+tools/plotting/venn_list.py
+tools/plotting/venn_list.txt
+tools/plotting/venn_list.xml
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.

diff -r 000000000000 -r baf7031d470e tools/plotting/venn_list.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/plotting/venn_list.xml Tue Jun 07 18:08:11 2011 -0400

@@ -0,0 +1,113 @@
+<tool id="venn_list" name="Venn Diagram" version="0.0.3">
+  <description>from lists</description>
+  <command interpreter="python">
+venn_list.py
+#if $universe.type_select=="implicit":
+  - -
+#else:
+  $main $main.ext
+#end if
+"$main_lab"
+#for $s in $sets:
+  $s.set $s.set.ext "$s.lab"
+#end for
+$PDF</command>
+  <inputs>
+    <param name="main_lab" size="30" type="text" value="Venn Diagram" label="Plot title"/>
+    <conditional name="universe">
+       <param name="type_select" type="select" label="Implicit or explicit full ID list?">
+         <option value="explicit">Explicit</option>
+         <option value="implicit">Implicit (use union of sets below)</option>
+       </param>
+       <when value="explicit">
+           <param name="main" type="data" format="tabular,fasta,fastq,sff" label="Full dataset (with all identifiers)" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
+       </when>
+       <when value="implicit"/>
+    </conditional>
+    <repeat name="sets" min="1" max="3" title="Sets">
+      <param name="set" type="data" format="tabular,fasta,fastq,sff" label="Members of set" help="Tabular file (uses column one), FASTA, FASTQ or SFF file."/>
+      <param name="lab" size="30" type="text" value="Group" label="Caption for set"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="PDF" />
+  </outputs>
+  <requirements>
+    <requirement type="python-module">rpy</requirement>
+    <requirement type="python-module">Bio</requirement>
+  </requirements>
+  <tests>
+    
+    
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**TIP:** If your data is in tabular files, the identifier is assumed to be in column one.
+
+**What it does**
+
+Draws Venn Diagram for one, two or three sets (as a PDF file).
+
+You must supply one, two or three sets of identifiers -- corresponding
+to one, two or three circles on the Venn Diagram.
+
+In general you should also give the full list of all the identifiers
+explicitly. This is used to calculate the number of identifers outside
+the circles (and check the identifiers in the other files match up).
+The full list can be omitted by implicitly taking the union of the
+category sets. In this case, the count outside the categories (circles)
+will always be zero.
+
+The identifiers can be taken from the first column of a tabular file
+(e.g. query names in BLAST tabular output, or signal peptide predictions
+after filtering, etc), or from a sequence file (FASTA, FASTQ, SFF).
+
+For example, you may have a set of NGS reads (as a FASTA, FASTQ or SFF
+file), and the results of several different read mappings (e.g. to
+different references) as tabular files (filtered to have just the mapped
+reads). You could then show the different mappings (and their overlaps)
+as a Venn Diagram, and the outside count would be the unmapped reads.
+
+**Citations**
+
+The Venn Diagrams are drawn using Gordon Smyth's limma package from
+R/Bioconductor, http://www.bioconductor.org/
+
+The R library is called from Python via rpy, http://rpy.sourceforge.net/
+
+This tool uses Biopython to read SFF files. If you use this tool with
+SFF files in scientific work leading to a publication, please cite the
+Biopython application note:
+
+Cock et al 2009. Biopython: freely available Python tools for computational
+molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
+http://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
+
+  </help>
+</tool>