Alignment.py

#!/usr/bin/python
# Copyright (C) 2013 Ion Torrent Systems, Inc. All Rights Reserved

import markdown
import operator
import os
import sys
import simplejson as json
from subprocess import *
from ion.plugin import *
from django.utils.datastructures import SortedDict

class Alignment(IonPlugin):
        # Whatever 'version' is set to will show up as the plugin's version in your browser.
        version = '3.6.5602'

        # The dictionary that holds environment variables; use it to keep a consistent environment.
        envDict = dict(os.environ)

        # This method performs the same actions found in the 'launch.sh' file. You don't need to make separate methods, but it is easier to organize.
        def analyze(self):
                # (See below for an explanation of Popen.)
                alignRead = Popen(['%s/alignment.py'%self.envDict['DIRNAME'], 'startplugin.json', self.envDict['TSP_LIBRARY'], self.envDict['TSP_FILEPATH_UNMAPPED_BAM'], self.envDict['TSP_FILEPATH_BAM']], stdout=PIPE, env=self.envDict)

                # Write results to a file.
                alignOut = open('%s/Alignment_API_output.txt'%self.envDict['TSP_FILEPATH_PLUGIN_DIR'], 'w')
                # <Popen var>.communicate() returns a tuple of [stdout, stderr] for that command. [0] gets the standard output, [1] gets the error output.
                alignOut.write(alignRead.communicate()[0])
                alignOut.close()
                # Copy the files.
                Popen(['cp', '-r', '%s/Alignment_block.php'%self.envDict['DIRNAME'], self.envDict['TSP_FILEPATH_PLUGIN_DIR']], stdout=PIPE, env=self.envDict)
                Popen(['cp', '-r', '%s/library'%self.envDict['DIRNAME'], self.envDict['TSP_FILEPATH_PLUGIN_DIR']], stdout=PIPE, env=self.envDict)

        # Method to launch the plugin.
        def launch(self, data=None):
                # Get json data.
                json_dat = getattr(self, 'startpluginjson', None)
                if not json_dat:
                        try:
                                with open('startplugin.json', 'r') as fh:
                                        json_dat = json.load(fh)
                        except:
                                sys.stderr.write('ERROR: could not read plugin json.')

                # Next, interpret the json. Store it in a sorted dictionary, and use markDOWN to format the markUP! (html)
                pluginjson = SortedDict()
                md = markdown.Markdown(extensions=['codehilite'], safe_mode='escape')
                for (k,v) in sorted(json_dat.iteritems()):
                        text = json.dumps(v, indent=2).split('\n')
                        text = '\n\t'.join(text)
                        html = md.convert(text)
                        pluginjson.insert(-1, k, html)

                # Update the context to hold the json data.
                context = { 'pluginjson' : pluginjson }
                self.context.update(context)

                # Do the analysis.
                self.analyze()

        # These methods are not necessary, but they are one way of reporting data.

        def report(self):
                pass

        def metric(self):
                pass

        # For debugging purposes.
        if __name__ == "__main__":
                PluginCLI(Alignment())