2018.01.26.1200

WARACS_BayesTraits.py

@@ -31,13 +31,13 @@
 __author__ = "Michael Gruenstaeudl, PhD <mi.gruenstaeudl@gmail.com>"
 __copyright__ = "Copyright (C) 2015 Michael Gruenstaeudl"
 __info__ = "Reconstructing Ancestral Character States using BayesTraits (http://www.evolution.reading.ac.uk/BayesTraits.html)"
-__version__ = "2015.12.15.1100"
+__version__ = "2018.01.26.1200"
 
 #############
 # DEBUGGING #
 #############
 
-#import pdb
+import pdb
 #pdb.set_trace()
 
 ####################
@@ -85,7 +85,8 @@ def main(treedistrFn, plottreeFn, charsFn, charnum, rcnmdl, pathToSoftware, keep
     # 1.4. Modify chars-file
     reader = csv.reader(open(charsFn, "r"), delimiter=",")
     arr = numpy.array(list(reader))
-    arr = arr[:,[0,charnum]]                                            # Extracting a particular column
+    #pdb.set_trace()
+    arr = arr[:,[0,int(charnum)]]                                       # Extracting a particular column
     out_handle = CSO.makeprettytable(arr)
     CFO.saveFile(charsFnTmp, out_handle)
 

suppl/CustomFileOps.py

@@ -0,0 +1,284 @@
+#!/usr/bin/env python
+"""General File Operations
+"""
+
+#####################
+# IMPORT OPERATIONS #
+#####################
+
+from __future__ import absolute_import
+from __future__ import print_function
+from six.moves import map
+from six.moves import input
+
+from subprocess import Popen, PIPE
+from pkg_resources import WorkingSet, DistributionNotFound
+import codecs
+import os
+import signal
+import sys
+import time
+
+###############
+# AUTHOR INFO #
+###############
+
+__author__ = "Michael Gruenstaeudl, PhD"
+__copyright__ = "Copyright (C) 2015 Michael Gruenstaeudl"
+__email__ = "mi.gruenstaeudl@gmail.com"
+__version__ = "2015.12.15.1100"
+
+#################
+# COMPATIBILITY #
+#################
+
+PY2 = sys.version_info[0] == 2
+PY3 = sys.version_info[0] == 3
+
+#############
+# DEBUGGING #
+#############
+
+#import pdb
+#pdb.set_trace()
+
+###########
+# CLASSES #
+###########
+
+class ListFilesInDir:
+    ''' Listing all files in directory.
+    Args:
+        string <a>
+    Returns:
+        list
+    '''
+    def __init__(self, a):
+        self.dr = a
+    def go(self):
+        return os.listdir(self.dr)
+
+class LoadFile:
+    ''' Loading input files.
+    Args:
+        string <a>, string <b>, string <c>
+    Returns:
+        string
+    '''
+    def __init__(self, a):
+        self.Fn = a
+    def openFile(self):
+        infile = open(self.Fn, "r").read()
+        return infile
+    def readLines(self):
+        infile = open(self.Fn, "r").read().splitlines()
+        return infile
+    def commaDelim(self):
+        infile = open(self.Fn, "r").read().split(",")
+        return infile
+
+class LoadModule:
+    ''' Loading module.
+    Args:
+        string <a>
+    Returns:
+        none
+    '''
+    def __init__(self, a):
+        self.inStr = a
+    def go(self):
+        import importlib
+        try:
+            list(map(__import__, [self.inStr]))
+            # except ImportError:                                   # Not all systems raise the exception "ImportError"; others raise different exception.
+        except:
+            print((sys.exc_info()[0]))
+            sys.exit("  ERROR: Please install the following Python packages: " + self.inStr)
+            # FUTURE CODE:
+            # CFO.installPkgs(self.inStr)
+        return importlib.import_module(self.inStr)
+
+class InstallPkgs:
+    ''' Automatically installing packages.
+    Args:
+        list <a> (example: ["dendropy", "numpy"])
+    Returns:
+        none
+    '''
+    def __init__(self, a):
+        self.pkgList = a
+
+    def go(self):
+        working_set = WorkingSet()
+        for pkgName in self.pkgList:
+            try:
+                depends = working_set.require(pkgName)
+            except DistributionNotFound:
+                from setuptools.command.easy_install import main as install
+                import urllib2
+                print("\n  Library '" + pkgName + "' needs to be installed.")
+                allow = input("  May I install the above library? ([y]/n): ")  # Prompt for user decision if a package requires installation
+                allow = allow.upper()
+                if allow == "N" or allow == "NO":
+                    sys.exit("\n  ERROR: Please install package '" + pkgName + "' manually.\n")
+                else:
+                    try:
+                        response = urllib2.urlopen("http://www.python.org/", timeout=10)
+                    except urllib2.URLError as err:
+                        sys.exit("\n  ERROR: No internet connection available.\n")
+                try:
+                    install(["--user", pkgName])                                # Make certain to use the user flag
+                    # ALTERNATIVE: os.system("easy_install-2.7 --user " + pkgName + "==" + pkgVersion)
+                    print("\n  Library '" + pkgName + "' installed successfully.")
+                    # ALTERNATIVE: print "\n  Library '" + pkgName + "v." + pkgVersion + "' installed successfully."
+                except:
+                    import os
+                    if sys.platform == "linux" or sys.platform == "linux2":
+                        if isExe("pip2.7"):
+                            os.system("pip2.7 install " + pkgName + " --user")
+                        else:
+                            ("\n  ERROR: Python setuptools inaccessible.\n")
+                    elif sys.platform == "darwin":
+                        if isExe("pip2.7"):
+                            os.system("pip2.7 install " + pkgName + " --user")
+                        else:
+                            ("\n  ERROR: Python setuptools inaccessible.\n")
+                    elif sys.platform == "win32":
+                        if isExe("pip2.7.exe"):
+                            os.system("pip2.7.exe install " + pkgName)
+                        else:
+                            ("\n  ERROR: Python setuptools inaccessible.\n")
+                try:
+                    exec("import " + pkgName)
+                except ImportError:
+                    sys.exit("\n  Please restart this script.\n")         # After installation via easy_install, Python must be restarted for certain new modules to be properly loaded
+                    #import os                                          # For later: Automatic restart
+                    #os.execv(__file__, sys.argv)
+
+class IsExe:
+    ''' Checking if executable exists. '''
+    def __init__(self, a):
+        self.fpath = a
+    def go(self):
+        return os.path.isfile(self.fpath) and os.access(self.fpath, os.X_OK)
+
+class PopenExtProg:
+    ''' Class for communicating with executable via Popen.
+    Args:
+        inlist <a>, flag <b>
+    Returns:
+        string
+    '''
+    def __init__(self, a, b):
+        self.cmdL = a
+        self.flag = b
+    def go(self):
+        initCmd = " ".join(self.cmdL)
+        if sys.platform == "linux" or sys.platform == "linux2" or sys.platform == "darwin":
+            p = Popen(initCmd, stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True, preexec_fn=os.setsid)
+            if self.flag:
+                time.sleep(float(self.flag))
+                os.killpg(p.pid, signal.SIGTERM)
+        if sys.platform == "win32":
+            p = Popen(initCmd, stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True)
+            if self.flag:
+                time.sleep(float(self.flag))
+                p.stdin.write("quit\n")
+        outStream, errorStream = p.communicate()
+        #if errorStream:                                                # too sensistive with many programs
+        #    sys.exit("  ERROR: ", self.err)
+        if PY2:
+            outStream = outStream
+        if PY3:
+            outStream = outStream.decode()                              # in Python 3, files are read as byte-like by default; need to decode to string
+        return outStream
+
+
+class RemoveFile:
+    ''' Deleting files.
+    Args:
+        string <a>
+    Returns:
+        none
+    '''
+    def __init__(self, a):
+        self.Fn = a
+    def go(self):
+        os.remove(self.Fn)
+
+
+class SaveFile:
+    ''' Saving data files.
+    Args:
+        string <a>, filehandle <b>, flag <c>
+    Returns:
+        none
+    '''
+    def __init__(self, a, b, c):
+        self.Fn = a
+        self.data = b
+        self.appendflag = c
+    def go(self):
+        if self.appendflag:
+            outfile = open(self.Fn, "a")
+        if not self.appendflag:
+            outfile = open(self.Fn, "w")
+        outfile.write(self.data)
+        outfile.close()
+
+class SaveFilewithDFN:
+    ''' Saving data files with filenames.
+    Args:
+        string <a>, filehandle <b>, string <c>
+    Returns:
+        none
+    '''
+    def __init__(self, a, b, c):
+        self.Fn = a
+        self.data = str(b)
+        self.info = c
+    def go(self):
+        outfile = open(self.Fn, "a")
+        outfile.write(self.info+"\n"+self.data+"\n")
+        outfile.close()
+
+###############
+# DEFINITIONS #
+###############
+
+def append(a, b):
+    return SaveFile(a, b, True).go()
+
+def deleteFile(a):
+    RemoveFile(a).go()
+
+def extprog(a, b=None):
+    return PopenExtProg(a, b).go()
+
+def installPkgs(pkgList):
+    InstallPkgs(pkgList).go()
+
+def isExe(a):
+    return IsExe(a).go()
+
+def listAllFilesInDir(a):
+    return ListFilesInDir(a).go()
+
+def loadCD(a):
+    return LoadFile(a).commaDelim()
+
+def saveFile(a, b):
+    return SaveFile(a, b, False).go()
+
+def saveFn(a, b, c):
+    return SaveFilewithDFN(a, b, c).go()
+
+def loadR(a):
+    return LoadFile(a).openFile()
+
+def loadRL(a):
+    return LoadFile(a).readLines()
+
+def loadModule(a):
+    return LoadModule(a).go()
+

suppl/CustomPhyloOps.py

@@ -0,0 +1,78 @@
+#!/usr/bin/env python
+"""Custom Phylo Operations
+"""
+
+#####################
+# IMPORT OPERATIONS #
+#####################
+
+from __future__ import absolute_import
+
+import CustomFileOps as CFO
+import sys
+
+dendropy = CFO.loadModule("dendropy")
+
+###############
+# AUTHOR INFO #
+###############
+
+__author__ = "Michael Gruenstaeudl, PhD"
+__copyright__ = "Copyright (C) 2015 Michael Gruenstaeudl"
+__email__ = "mi.gruenstaeudl@gmail.com"
+__version__ = "2015.12.15.1100"
+
+#############
+# DEBUGGING #
+#############
+
+#import pdb
+#pdb.set_trace()
+
+###########
+# CLASSES #
+###########
+
+class convertNexusToNewick:
+    ''' Convert a phylogenetic tree in NEXUS format to a phylogenetic tree in NEWICK format
+    Args:
+        string <a>
+    Returns:
+        string
+    '''
+    def __init__(self, a):
+        self.inStr = a
+    def go(self):
+        treeH = dendropy.Tree.get_from_string(self.inStr, schema="nexus")
+        return treeH.as_string(schema='newick')
+
+class getNodeListFromTree:
+    ''' class for generating a list of nodes from a phylogenetic tree
+    Args:
+        string <a>
+    Returns:
+        str, list
+    '''
+    def __init__(self, a):
+        self.inFn = a
+    def go(self):
+        nodespecL, nodeL = [], []
+        treeH = dendropy.Tree.get_from_path(self.inFn, schema="nexus")
+        for c, node in enumerate(treeH.nodes(), start=1):
+            tips = [tip.taxon.label.replace(" ", "_") for tip in node.leaf_nodes()]
+            if len(tips) > 1:
+                nodespecL.append("AddNode Node" + str(c) + " " + " ".join(tips))
+                nodeL.append(c)                                         # generate list of relevant node numbers
+        node_specs = "\n".join(nodespecL)
+        return [node_specs, nodeL]
+
+###############
+# DEFINITIONS #
+###############
+
+def ConvertNexusToNewick(a):
+    return convertNexusToNewick(a).go()
+
+
+def GetNodeListFromTree(a):
+    return getNodeListFromTree(a).go()