Mercurial > repos > malex > beast

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beast/beast.py	Tue Apr 17 10:52:00 2012 -0400
@@ -0,0 +1,128 @@
+#!/usr/bin/env python
+
+"""
+Copyright 2012 Oleksandr Moskalenko <om@hpc.ufl.edu>
+
+Runs BEAST on an input XML file.
+For use with BEAST version 1.7.1
+
+usage: beast.py inputxml
+
+Produces:
+    output log file
+    mcmc.operators file
+    A variable number of '.tree' files depending on the XML input
+"""
+import os, shutil, subprocess, sys, optparse, glob, string
+
+def stop_err(msg):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit()
+
+def __main__():
+    usage = "usage: %prog inputXML"
+    parser = optparse.OptionParser(usage = usage)
+    parser.add_option("-T", "--threads", action="store", type="string", dest="threads", help="Number of threads")
+    parser.add_option("-s", "--seed", action="store", type="string",
+            dest="seed", help="Random seed")
+    parser.add_option("-r", "--strict", action="store_true", dest="strict", help="Strict XML parsing")
+    parser.add_option("-e", "--errors", action="store", type="string",
+            dest="errors", help="Maximum number of errors allowed")
+    parser.add_option("-i", "--inputxml", action="store", type="string", dest="inputxml", help="Input XML")
+    parser.add_option("-o", "--operators", action="store", type="string", dest="operators", help="Operators")
+    parser.add_option("-l", "--logs", action="store", type="string", dest="logs", help="Logs")
+    parser.add_option("-t", "--trees", action="store", type="string", dest="trees", help="Trees")
+    parser.add_option("-d", "--id", action="store", type="string", dest="treeid", help="Tree ID")
+    parser.add_option("-p", "--path", action="store", type="string", dest="path", help="New file path")
+    (options, args) = parser.parse_args()
+    if options.threads == None:
+        threads = 1
+    else:
+        threads = int(options.threads)
+    if options.seed != None:
+        seed = int(options.seed)
+    else:
+        seed = 12345
+    if options.strict == "-strict":
+        print "Strict XML check was chosen\n"
+        strict = True
+        print "No strict XML check was chosen\n"
+    else:
+        strict = False
+    inputxml = options.inputxml
+    operators = options.operators
+    logs = options.logs
+    trees = options.trees
+    errors = options.errors
+    treefile_id = options.treeid
+    newfilepath = options.path
+    sys.stdout.write("The following parameters have been provided:\n")
+    sys.stdout.write("Input XML: %s\n" % inputxml)
+    sys.stdout.write("Operators: %s\n" % operators)
+    sys.stdout.write("Logs: %s\n" % logs)
+    sys.stdout.write("Trees: %s\n" % trees)
+    sys.stdout.write("Strict: %s\n" % strict)
+    sys.stdout.write("New file path: %s\n" % newfilepath)
+    sys.stdout.write("Tree file ID: %s\n" % treefile_id)
+    if errors != None:
+        sys.stdout.write("Errors: %s\n" % errors)
+    cmd = []
+    cmd.append('beast')
+    if strict == True:
+        cmd.append('-strict')
+    thread_opt = "-threads %d" % threads
+    sys.stdout.write("Threads: %s\n" % thread_opt)
+    cmd.append(thread_opt)
+    cmd.append('-seed %d' % int(seed))
+    if errors != None:
+        cmd.append('-errors %d' % int(errors))
+    cmd.append(inputxml)
+    try:
+        proc = subprocess.Popen(args=cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        sys.stderr.write("Error invoking command: \n%s\n\n%s\n" % (cmd, err))
+        sys.exit(1)
+    stdout, stderr = proc.communicate()
+    return_code = proc.returncode
+    if return_code:
+        sys.stdout.write(stdout)
+        sys.stderr.write(stderr)
+        sys.stderr.write("Return error code %i from command:\n" % return_code)
+        sys.stderr.write("%s\n" % cmd)
+        sys.exit(1)
+    else:
+        sys.stdout.write(stdout)
+        sys.stdout.write(stderr)
+    try:
+        for logfile in glob.glob('*.log'):
+            shutil.copyfile(os.path.basename(logfile), 'beast.log')
+    except Exception, err:
+        sys.stderr.write("Error copying log file: \n%s\n" % err)
+    try:
+        if not os.path.exists('mcmc.operators'):
+            bat = open('mcmc.operators','w')
+            bat.write('The mcmc.operators file did not have any output.\n')
+            bat.close()
+    except Exception, err:
+        sys.stderr.write("Error copying mcmc.operators file: \n%s\n" % err)
+    try:
+        treefiles_orig = glob.glob('*.trees')
+        if len(treefiles_orig) == 0:
+            treefiles_orig.append('Error_no_tree')
+            dummy_file = open('Error_no_tree','w')
+            dummy_file.write("BEAST run has not produced an output tree\n")
+            dummy_file.close()
+        treefiles = []
+        if os.path.isdir(newfilepath):
+            for filename in treefiles_orig:
+                if os.path.isfile(filename):
+                    name = string.replace(os.path.splitext(filename)[0], "_", "-")
+                    filestring = "primary_%s_%s_visible_nexus" % (treefile_id, name)
+                    newpath = os.path.join(newfilepath,filestring)
+                    treefiles.append(newpath)
+        treefiles[0] = trees
+        for i in range(len(treefiles_orig)):
+            shutil.move(treefiles_orig[i], treefiles[i])
+    except Exception, err:
+        sys.stderr.write("Error copying trees file(s): \n%s\n" % err)
+if __name__=="__main__": __main__()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/beast/beast.xml	Tue Apr 17 10:52:00 2012 -0400
@@ -0,0 +1,65 @@
+<tool id="beast" name="Beast" version="1.0" force_history_refresh="True">
+  <description>Bayesian MCMC analysis of molecular sequences.</description>
+  <version_command>beast 2> /dev/null | grep -e "v[0-9]\.*" | awk '{print $2}' | awk -F, '{print $1}' | sed 's/^.//'</version_command>
+  <command interpreter="python">beast.py -T 4 -r $strict -s $seed -i $inputxml -o $operators -l $log -t $trees -d $trees.id -p $__new_file_path__</command>
+  <inputs>
+    <param format="xml" name="inputxml" type="data">
+      <label>Input XML File</label>
+    </param>
+    <param name="strict" type="boolean" checked="no" truevalue="-strict" falsevalue="" display="checkboxes">
+        <label>Fail on non-conforming BEAST XML</label>
+    </param>
+    <param name="seed" size="8" type="integer" value="12345" label="Random Seed">
+    </param>
+    <param name="errors" size="4" type="integer" value="1000" label="Maxium number of numerical errors before stopping">
+    </param>
+  </inputs>
+  <outputs>
+    <data format="txt" name="operators" label="${tool.name} on ${on_string}: Operators " from_work_dir="mcmc.operators"/>
+    <data format="txt" name="log" label="${tool.name} on ${on_string}: Log" from_work_dir="beast.log"/>
+    <data format="nexus" name="trees" label="${tool.name} on ${on_string}: Trees" />
+  </outputs>
+<help>
+.. class:: warningmark
+
+The input dataset needs to be in BEAST XML format.
+
+If the random seed is not chosen "12345" will be used.
+
+-----
+
+**BEAST v1.7.1, 2002-2012**
+
+Bayesian Evolutionary Analysis Sampling Trees
+
+Designed and developed by
+
+
+Alexei J. Drummond -
+Department of Computer Science,
+University of Auckland,
+alexei@cs.auckland.ac.nz
+
+Andrew Rambaut -
+Institute of Evolutionary Biology,
+University of Edinburgh,
+a.rambaut@ed.ac.uk
+
+Marc A. Suchard - David Geffen School of Medicine,
+University of California, Los Angeles,
+msuchard@ucla.edu
+
+Downloads, Help and Resources: http://beast.bio.ed.ac.uk
+
+Source code distributed under the GNU Lesser General Public License:
+http://code.google.com/p/beast-mcmc
+
+BEAST developers:
+Alex Alekseyenko, Trevor Bedford, Erik Bloomquist, Joseph Heled, Sebastian
+Hoehna, Denise Kuehnert, Philippe Lemey, Wai Lok Sibon Li, Gerton Lunter,
+Sidney Markowitz, Vladimir Minin, Michael Defoin Platel, Oliver Pybus,
+Chieh-Hsi Wu, Walter Xie
+
+Thanks to: Roald Forsberg, Beth Shapiro and Korbinian Strimmer
+</help>
+</tool>