diff Bed.py @ 2:4ced8f116509 draft

planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 23b12dd763c0235674988ebdf6a258afd1ad629a-dirty

--- a/Bed.py	Tue Nov 22 17:07:47 2016 -0500
+++ b/Bed.py	Tue Nov 22 17:13:18 2016 -0500
@@ -26,13 +26,10 @@
         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
@@ -42,10 +39,8 @@
         with open(myBigBedFilePath, 'w') as self.bigBedFile:
             subtools.bedToBigBed(self.sortedBedFile.name,
                                  self.chromSizesFile.name,
-                                 self.bigBedFile.name,
-                                 typeOption='bed12+1',
-                                 tab=True)
-        
+                                 self.bigBedFile.name)
+
         # Create the Track Object
         self.createTrack(file_path=trackName,
                          track_name=trackName,
@@ -53,8 +48,7 @@
                          priority=self.priority,
                          track_file=myBigBedFilePath,
                          track_color=self.track_color,
-                         group_name=self.group_name,
-                         )
+                         group_name=self.group_name)
 
         # dataURL = "tracks/%s" % trackName
         #
@@ -76,35 +70,4 @@
         # )
 
         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   
\ No newline at end of file