# HG changeset patch
# User peterjc
# Date 1559119519 14400
# Node ID 679b6323db0303d280e296ec78830511dc6a1311
# Parent  20d347feb8828df349dcb0934007f393ea7a3046
v0.1.0 now using matplotlib_venn instead of limma R package via rpy. Contribution from Frederic Sapet.

diff -r 20d347feb882 -r 679b6323db03 tools/venn_list/README.rst
--- a/tools/venn_list/README.rst	Thu May 11 07:02:57 2017 -0400
+++ b/tools/venn_list/README.rst	Wed May 29 04:45:19 2019 -0400
@@ -33,8 +33,8 @@
 The suggested location is in the Galaxy folder ``tools/plotting`` next to other
 graph drawing tools, or a dedicated ``tools/venn_list`` directory.
 
-You will also need to install Biopython 1.54 or later, and the R/Bioconductor
-package limma. You should already have rpy installed for other Galaxy tools.
+You will also need to install Biopython 1.54 or later, matplotlib, and
+matplotlib_venn - all available via PyPI or Conda,
 
 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
@@ -79,6 +79,10 @@
         - Single quote command line arguments (internal change only)
         - Python 3 compatible print function.
         - Capture python script version when run from Galaxy.
+v0.0.12 - Internal Python style change.
+        - Python 3 compatible exception handling.
+v0.1.0  - Now uses Python library matplotlib_venn to draw the diagram
+          instead of R's limma via rpy). Contribution from Frederic Sapet.
 ======= ======================================================================
 
 
@@ -107,7 +111,7 @@
 
     $ planemo shed_upload --tar_only tools/venn_list/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     tools/venn_list/README.rst
     tools/venn_list/tool_dependencies.xml
     tools/venn_list/venn_list.py
diff -r 20d347feb882 -r 679b6323db03 tools/venn_list/tool_dependencies.xml
--- a/tools/venn_list/tool_dependencies.xml	Thu May 11 07:02:57 2017 -0400
+++ b/tools/venn_list/tool_dependencies.xml	Wed May 29 04:45:19 2019 -0400
@@ -1,15 +1,15 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="galaxy_sequence_utils" version="1.0.1">
-        <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="c1ab450748ba" name="package_galaxy_sequence_utils_1_0_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="limma" version="3.25.3">
-        <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b19c06e97bce" name="package_r2_limma_3_25_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="rpy" version="1.0.3">
-        <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="82170c94ca7c" name="package_rpy_1_0_3" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a12f73c3b116" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file
diff -r 20d347feb882 -r 679b6323db03 tools/venn_list/venn_list.py
--- a/tools/venn_list/venn_list.py	Thu May 11 07:02:57 2017 -0400
+++ b/tools/venn_list/venn_list.py	Wed May 29 04:45:19 2019 -0400
@@ -1,5 +1,9 @@
 #!/usr/bin/env python
-"""Plot up to 3-way Venn Diagram using R limma vennDiagram (via rpy)
+
+"""
+Plot up to 3-way Venn Diagram.
+
+It uses the Python libraries matplotlib and matplotlib_venn.
 
 This script is copyright 2010-2017 by Peter Cock, The James Hutton Institute
 (formerly SCRI), UK. All rights reserved.
@@ -10,26 +14,25 @@
 from __future__ import print_function
 
 import sys
+from shutil import move
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print("v0.0.11")
+    print("v0.1.0")
     sys.exit(0)
 
 try:
-    import rpy
+    import matplotlib
 except ImportError:
-    sys.exit("Requires the Python library rpy (to call R)")
-except RuntimeError, e:
-    sys.exit("The Python library rpy is not availble for the current R version\n\n%s" % e)
+    sys.exit("Requires the Python library matplotlib")
 
-try:
-    rpy.r.library("limma")
-except Exception:
-    sys.exit("Requires the R library limma (for vennDiagram function)")
-
+matplotlib.use("Agg")
+from matplotlib import pyplot as plt
 
 if len(sys.argv) - 1 not in [7, 10, 13]:
-    sys.exit("Expected 7, 10 or 13 arguments (for 1, 2 or 3 sets), not %i" % (len(sys.argv) - 1))
+    sys.exit(
+        "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 = []
@@ -45,6 +48,7 @@
 
 
 def load_ids(filename, filetype):
+    """Load ids from files."""
     if filetype == "tabular":
         for line in open(filename):
             line = line.rstrip("\n")
@@ -57,6 +61,7 @@
     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.
@@ -68,18 +73,21 @@
         except ImportError:
             sys.exit("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
+        for this_name in index(filename, "sff"):
+            yield this_name
     else:
         sys.exit("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
+    """Check if ids are in whitelist."""
+    for single_name in load_ids(filename, filetype):
+        if single_name in whitelist:
+            yield single_name
         else:
-            sys.exit("Unexpected ID %s in %s file %s" % (name, filetype, filename))
+            sys.exit(
+                "Unexpected ID %s in %s file %s" % (single_name, filetype, filename)
+            )
 
 
 if all_file in ["", "-", '""', '"-"']:
@@ -98,42 +106,54 @@
 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
+names = [one_name for one_file, one_type, one_name in set_data]
+lengths = [len(one_set) for one_set in sets]
+
+if len(sets) == 3:
+    try:
+        from matplotlib_venn import venn3_unweighted
+    except ImportError:
+        sys.exit("Requires the Python library matplotlib_venn")
+    venn3_unweighted(
+        sets,
+        [
+            "{} (Total {})".format(name, length)
+            for (name, length) in zip(names, lengths)
+        ],
+    )
+
+if len(sets) == 2:
+    try:
+        from matplotlib_venn import venn2_unweighted
+    except ImportError:
+        sys.exit("Requires the Python library matplotlib_venn")
+    venn2_unweighted(
+        sets,
+        [
+            "{} (Total {})".format(name, length)
+            for (name, length) in zip(names, lengths)
+        ],
+    )
+
+# not sure what I am doing here,
+# matplotlib_venn does not want to create a single Venn circle
+# stick to the old behavior (rpy and Limma) as much as possible
+if len(sets) == 1:
+    try:
+        from matplotlib_venn import venn2
+    except ImportError:
+        sys.exit("Requires the Python library matplotlib_venn")
+    venn2((sets[0], set()), [set_data[0][2], ""])
+
+plt.title(all_label)
+plt.savefig(pdf_file + ".pdf")
+
+# Format "dat" is not supported.
 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_ids
-        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_ids)))
-    rpy.r.dev_off()
-except Exception, exc:
-    sys.exit("%s" % str(exc))
-rpy.r.quit(save="no")
+    move(pdf_file + ".pdf", pdf_file)
+except (OSError, IOError) as error:
+    sys.exit("Fail to rename file {}".format(str(error)))
+
+plt.close()
+
 print("Done")
diff -r 20d347feb882 -r 679b6323db03 tools/venn_list/venn_list.xml
--- a/tools/venn_list/venn_list.xml	Thu May 11 07:02:57 2017 -0400
+++ b/tools/venn_list/venn_list.xml	Wed May 29 04:45:19 2019 -0400
@@ -1,10 +1,10 @@
-<tool id="venn_list" name="Venn Diagram" version="0.0.11">
+<tool id="venn_list" name="Venn Diagram" version="0.1.0">
     <description>from lists</description>
     <requirements>
-        <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement>
-        <requirement type="package" version="1.0.3">rpy</requirement>
-        <requirement type="package" version="3.25.3">limma</requirement>
+        <requirement type="package" version="1.1.3">galaxy_sequence_utils</requirement>
         <requirement type="package" version="1.67">biopython</requirement>
+        <requirement type="package" version="2.0.0">matplotlib</requirement>
+        <requirement type="package" version="0.11.5">matplotlib-venn</requirement>
     </requirements>
     <version_command>
 python $__tool_directory__/venn_list.py --version
@@ -126,10 +126,9 @@
 
 **Citations**
 
-The Venn Diagrams are drawn using Gordon Smyth's limma package from
-R/Bioconductor, http://www.bioconductor.org/
+The Venn Diagrams are drawn using Konstantin Tretyakov's matplotlib-venn
+package, https://pypi.org/project/matplotlib-venn/
 
-The R library is called from Python via rpy, http://rpy.sourceforge.net/
 
 If you use this Galaxy tool in work leading to a scientific publication please
 cite:
@@ -137,14 +136,14 @@
 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
 Galaxy tools and workflows for sequence analysis with applications
 in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
+https://doi.org/10.7717/peerj.167
 
 This tool uses Biopython to read and write SFF files, so you may also wish to
 cite the Biopython application note (and Galaxy too of course):
 
 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.
+https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.
 
     </help>
     <citations>