comparison TrackHub.py @ 50:3e5b6f6a9abe draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 6391cdb975d14b5a7060fa1665a8a575797a0eaa-dirty

49:193e94a43f0f

#!/usr/bin/env python

import os
import subprocess
import shutil
import utils


class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData):

        print "Success!\n"
    
    def prepareRefseq(self):
        try:
            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
            p = subprocess.Popen(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
            # Wait for process to terminate.
            p.communicate()
        except OSError as e:
            print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
    #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
    def addTrack(self, track):
        #print "false_path" , track['false_path']

            self.Bam(track, metadata)
           # print "add bam track\n"
        elif track['dataType'] == 'bigwig':
            self.BigWig(track, metadata)
        else: 
            gff3_file = os.path.join(self.raw, track['fileName'])
            if track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            elif track['dataType'] == 'gff3_transcript':
                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            else:
                p = subprocess.Popen(['flatfile-to-json.pl', '--gff', gff3_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            p.communicate()
            
    def indexName(self):
        p = subprocess.Popen(['generate-names.pl', '-v', '--out', self.json])
        p.communicate()
        print "finished name index \n"

    def makeArchive(self):
        shutil.make_archive(self.out_path, 'zip', self.out_path)
        data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'

                else:
                    os.remove(data_folder)
        except OSError as oserror:
            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
        shutil.copytree(self.out_path, data_folder)
        p = subprocess.Popen(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
        p.communicate()
        shutil.rmtree(self.out_path)
    
    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
    #run it locally. May need modify
    def outHtml(self):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            zipfiles = '<li><a href = "%s">Download</a></li>'
            jbrowse_hub = '<li><a href = "http://192.168.56.11/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
            filedir_abs = os.path.abspath(self.outfile)
            filedir = os.path.dirname(filedir_abs)
            filedir = os.path.join(filedir, self.outfolder)
            for root, dirs, files in os.walk(filedir):
                for file in files:

        bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
        bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
        bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
        bam_track['label'] = metadata['label']
        bam_track['category'] = metadata['category']
        utils.add_tracks_to_json(json_file, bam_track, 'add_tracks')

    def BigWig(self, track, metadata):
        #create trackList.json if not exist
        self.createTrackList()
        json_file = os.path.join(self.json, "trackList.json")
        bigwig_track = dict()

        bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
        bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
        bigwig_track['label'] = metadata['label']
        bigwig_track['style'] = metadata['style']
        bigwig_track['category'] = metadata['category']
        utils.add_tracks_to_json(json_file, bigwig_track, 'add_tracks')

    #If the metadata is not set, use the default value
    def SetMetadata(self, track, metadata):
        if 'label' not in metadata.keys() or metadata['label'] == '':
            metadata['label'] = track['fileName']

            metadata['color'] = "#daa520"
        if track['dataType'] == 'bigwig':
            if 'style' not in metadata.keys():
                metadata['style'] = {}
            if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
                metadata['pos_color'] = "#FFA600"
            if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
                metadata['neg_color'] = "#005EFF"
        if 'category' not in metadata.keys() or metadata['category'] == '':
            metadata['category'] = "Default group"
        if track['dataType'] == 'blastxml':
            metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
        elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':

50:3e5b6f6a9abe

#!/usr/bin/env python

import os
import subprocess
import shutil
import json
import utils


class TrackHub:
    def __init__(self, inputFiles, reference, outputDirect, tool_dir, genome, extra_files_path, metaData):

        print "Success!\n"
    
    def prepareRefseq(self):
        try:
            #print os.path.join(self.tool_dir, 'prepare-refseqs.pl') + ", '--fasta', " + self.reference +", '--out', self.json])"
            subprocess.call(['prepare-refseqs.pl', '--fasta', self.reference, '--out', self.json])
        except OSError as e:
            print "Cannot prepare reference error({0}): {1}".format(e.errno, e.strerror)
    #TODO: hard coded the bam and bigwig tracks. Need to allow users to customize the settings
    def addTrack(self, track):
        #print "false_path" , track['false_path']

            self.Bam(track, metadata)
           # print "add bam track\n"
        elif track['dataType'] == 'bigwig':
            self.BigWig(track, metadata)
        else: 
            flat_file = os.path.join(self.raw, track['fileName'])
            if track['dataType'] == 'bed':
                subprocess.call(['flatfile-to-json.pl', '--bed', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            elif track['dataType'] == 'bedSpliceJunctions' or track['dataType'] == 'gtf' or track['dataType'] == 'blastxml':
                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"glyph": "JBrowse/View/FeatureGlyph/Segments", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            elif track['dataType'] == 'gff3_transcript':
                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"transcriptType": "transcript", "category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            else:
                subprocess.call(['flatfile-to-json.pl', '--gff', flat_file, '--trackType', metadata['type'], '--trackLabel', metadata['label'], '--Config', '{"category" : "%s"}' % metadata['category'], '--clientConfig', '{"color" : "%s"}' % metadata['color'], '--out', self.json])
            
    def indexName(self):
        subprocess.call(['generate-names.pl', '-v', '--out', self.json])
        print "finished name index \n"

    def makeArchive(self):
        shutil.make_archive(self.out_path, 'zip', self.out_path)
        data_folder = '/var/www/html/JBrowse-1.12.1/jbrowse_hub'

                else:
                    os.remove(data_folder)
        except OSError as oserror:
            print "Cannot create data folder({0}): {1}".format(oserror.errno, oserror.strerror)
        shutil.copytree(self.out_path, data_folder)
        subprocess.call(['chmod', '-R', 'o+rx', '/var/www/html/JBrowse-1.12.1/jbrowse_hub'])
        shutil.rmtree(self.out_path)
    
    #TODO: this will list all zip files in the filedir and sub-dirs. worked in Galaxy but all list zip files in test-data when
    #run it locally. May need modify
    def outHtml(self):
        with open(self.outfile, 'w') as htmlfile:
            htmlstr = 'The JBrowse Hub is created: <br>'
            zipfiles = '<li><a href = "%s">Download</a></li>'
            jbrowse_hub = '<li><a href = "/static/JBrowse-1.12.1/index.html?data=jbrowse_hub/json" target="_blank">View JBrowse Hub</a></li>'
            filedir_abs = os.path.abspath(self.outfile)
            filedir = os.path.dirname(filedir_abs)
            filedir = os.path.join(filedir, self.outfolder)
            for root, dirs, files in os.walk(filedir):
                for file in files:

        bam_track['storeClass'] = 'JBrowse/Store/SeqFeature/BAM'
        bam_track['urlTemplate'] = os.path.join('../raw', track['fileName'])
        bam_track['baiUrlTemplate'] = os.path.join('../raw', track['index'])
        bam_track['label'] = metadata['label']
        bam_track['category'] = metadata['category']
        bam_track = json.dumps(bam_track)
        #Use add-track-json.pl to add bam track to json file
        new_track = subprocess.Popen(['echo', bam_track], stdout=subprocess.PIPE)
        subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)
    
    def BigWig(self, track, metadata):
        #create trackList.json if not exist
        self.createTrackList()
        json_file = os.path.join(self.json, "trackList.json")
        bigwig_track = dict()

        bigwig_track['type'] = 'JBrowse/View/Track/Wiggle/XYPlot'
        bigwig_track['storeClass'] = 'JBrowse/Store/SeqFeature/BigWig'
        bigwig_track['label'] = metadata['label']
        bigwig_track['style'] = metadata['style']
        bigwig_track['category'] = metadata['category']
        bigwig_track = json.dumps(bigwig_track)
        #Use add-track-json.pl to add bigwig track to json file
        new_track = subprocess.Popen(['echo', bigwig_track], stdout=subprocess.PIPE)
        #output = new_track.communicate()[0]
        subprocess.call(['add-track-json.pl', json_file], stdin=new_track.stdout)

    #If the metadata is not set, use the default value
    def SetMetadata(self, track, metadata):
        if 'label' not in metadata.keys() or metadata['label'] == '':
            metadata['label'] = track['fileName']

            metadata['color'] = "#daa520"
        if track['dataType'] == 'bigwig':
            if 'style' not in metadata.keys():
                metadata['style'] = {}
            if 'pos_color' not in metadata['style'] or metadata['style']['pos_color'] == '':
                metadata['style']['pos_color'] = "#FFA600"
            if 'neg_color' not in metadata['style'] or metadata['style']['neg_color'] == '':
                metadata['style']['neg_color'] = "#005EFF"
        if 'category' not in metadata.keys() or metadata['category'] == '':
            metadata['category'] = "Default group"
        if track['dataType'] == 'blastxml':
            metadata['type'] = "G-OnRamp_plugin/BlastAlignment"
        elif track['dataType'] == 'gff3_transcript' or track['dataType'] == 'gff3_mrna':