view Bed.py @ 0:3e0c61b52a06 draft

planemo upload for repository https://github.com/Yating-L/hub-archive-creator commit a77635b40ebd29baafb3bea57f8cbfb3f252e3b0-dirty

#!/usr/bin/python

import os
import tempfile

# Internal dependencies
from Datatype import Datatype
from Track import Track
from TrackDb import TrackDb
from util import subtools


class Bed( Datatype ):
    def __init__( self, inputBedGeneric, data_bed_generic):
        super(Bed, self).__init__()

        self.track = None

        self.inputBedGeneric = inputBedGeneric

        self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")

        self.data_bed_generic = data_bed_generic
        self.name_bed_generic = self.data_bed_generic["name"]
        self.priority = self.data_bed_generic["order_index"]
        self.track_color = self.data_bed_generic["track_color"]
        # TODO: Think about how to avoid repetition of the group_name everywhere
        self.group_name = self.data_bed_generic["group_name"]
   
        modified = self._checkAndFixBed()
        # Sort processing
        subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
        
       


        # bedToBigBed processing
        # TODO: Change the name of the bb, to tool + genome + possible adding if multiple +  .bb
        trackName = "".join( ( self.name_bed_generic, ".bb") )

        myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
        with open(myBigBedFilePath, 'w') as self.bigBedFile:
            subtools.bedToBigBed(self.sortedBedFile.name,
                                 self.chromSizesFile.name,
                                 self.bigBedFile.name,
                                 typeOption='bed12+1',
                                 tab=True)
        
        # Create the Track Object
        self.createTrack(file_path=trackName,
                         track_name=trackName,
                         long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
                         priority=self.priority,
                         track_file=myBigBedFilePath,
                         track_color=self.track_color,
                         group_name=self.group_name,
                         )

        # dataURL = "tracks/%s" % trackName
        #
        # trackDb = TrackDb(
        #     trackName=trackName,
        #     longLabel=self.name_bed_generic,
        #     shortLabel=self.getShortName(self.name_bed_generic),
        #     trackDataURL=dataURL,
        #     trackType='bigBed',
        #     visibility='dense',
        #     thickDrawItem='on',
        #     priority=self.priority,
        # )
        #
        # # Return the BigBed track
        # self.track = Track(
        #     trackFile=myBigBedFilePath,
        #     trackDb=trackDb,
        # )

        print("- Bed %s created" % self.name_bed_generic)
        if (len(modified) != 0):
            print("The lines that were removed: " + str(len(modified)))
        #print("- %s created in %s" % (trackName, myBigBedFilePath))

    # TODO: bed verifier, check if there are invalid strands: "." 
    def _checkAndFixBed(self):
        """
        Call _checkAndFixBed, check the integrity of bed file, 
        if the strand is not "+" or "-" truncate that line and report to users
        create  column and move the score column to
        """
        # Store the lines that have been removed 
        removedLines = []
        # Remove the lines with invalid strand
        temp_bed = tempfile.NamedTemporaryFile(bufsize=0, suffix=".bed", delete=False)
        with open(temp_bed.name, 'w') as tmp:
            with open(self.inputBedGeneric, 'r') as f:
                lines = f.readlines()
                for line in lines:
                    fields = line.split()
                    strand = fields[5]
                    score = fields[4]
                    fields[4] = '1000'
                    fields.append(score)
                    if (strand == '+' or strand == '-'):
                        tmp.write('\t'.join(map(str, fields)))
                        tmp.write("\n")
                    else:
                        removedLines.append(line)
        self.inputBedGeneric = temp_bed.name
            
        return removedLines