Mercurial > repos > malex > beast
changeset 2:1914e55fee82 draft
Deleted selected files
| author | malex |
|---|---|
| date | Thu, 26 Apr 2012 11:11:00 -0400 |
| parents | 677344fb75c1 |
| children | 95b13782906c |
| files | beast/beast.py beast/beast.xml |
| diffstat | 2 files changed, 0 insertions(+), 243 deletions(-) [+] |
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--- a/beast/beast.py Thu Apr 26 11:08:35 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ -#!/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 -from xml.dom.minidom import parse, Node - -def stop_err(msg): - sys.stderr.write("%s\n" % msg) - sys.exit() - -def parseFnames(nodelist): - filenames = [] - for node in nodelist: - if node.hasAttributes(): - fname = node.getAttribute('fileName') - if fname != "": - filenames.append(fname) - else: - pass - return filenames - -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) -#2012-04-24 - 2nd approach, parse the .xml file: - xml_file = os.path.abspath(inputxml) - if not os.path.exists(inputxml): - sys.stderr.write("Cannot find the input XML file for parsing.\n") - dom = parse(inputxml) - xml_logs = dom.getElementsByTagName('log') - xml_trees = dom.getElementsByTagName('logTree') - logfiles_orig = parseFnames(xml_logs) - treefiles_orig = parseFnames(xml_trees) - try: - if len(logfiles_orig) == 0: - logfiles_orig = glob.glob("*.log*") - if len(logfiles_orig) == 0: - logfiles_orig.append('Error_no_log') - dummy_file = open('Error_no_log','w') - dummy_file.write("BEAST run has not produced a log or it's named in such a way that I can't locate it. Configure BEAST to produce .log files without spaces in their names and rerun the analysis.\n") - dummy_file.close() - logfiles = [] - if os.path.isdir(newfilepath): - for filename in logfiles_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) - logfiles.append(newpath) -# else: -# sys.stderr.write("Can't find the log file to rename.\n") - logfiles[0] = logs - for i in range(len(logfiles_orig)): - src = logfiles_orig[i] - dst = logfiles[i] - if os.path.exists(src): - shutil.copy(src, dst) -# else: -# print "File '%s' can't be found.\n" % src - 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: - if len(treefiles_orig) == 0: - print "No tree files found by the xml file parser.\n" - treefiles_orig = glob.glob("*.trees*") -# print "Original tree files from the directory:\n\t%s" % " ".join(treefiles_orig) - 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 or it's named in such a way that I can't locate it. Configure BEAST to produce .tree files without spaces in their names and rerun the analysis.\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)): - src = treefiles_orig[i] - dst = treefiles[i] - if os.path.exists(src): - shutil.copy(src, dst) - except Exception, err: - sys.stderr.write("Error copying trees file(s): \n%s\n" % err) -if __name__=="__main__": __main__()
--- a/beast/beast.xml Thu Apr 26 11:08:35 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,65 +0,0 @@ -<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. The names of the log output files configured in the xml file should have the '.log' extension and the trees file(s) should have the '.tree' extension for the best presentation. - -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>