diff smart_toolShed/commons/core/writer/WigWriter.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/writer/WigWriter.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,139 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+from commons.core.writer.TranscriptListWriter import TranscriptListWriter
+
+
+class WigWriter(TranscriptListWriter):
+    """
+    A class that writes a transcript list into a file with WIGGLE format
+    @ivar fileName: name of the file 
+    @type fileName: string
+    @ivar handle: handle to the file
+    @type handle: file handle
+    @ivar header: first lines of the file
+    @type header: string
+    """
+
+
+    def __init__(self, fileName, verbosity = 0):
+        """
+        Constructor
+        @param fileName: name of the file 
+        @type fileName: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        self.fileName  = fileName
+        self.verbosity = verbosity
+        self.data      = {-1: {}, 0: {}, 1: {}}
+        self.title     = "Reads"
+        self.strands   = False
+        self.handle    = None
+
+
+    def __del__(self):
+        """
+        Destructor
+        Actually print the file
+        """
+        strand2string = {-1: "-", 1: "+", 0: ""}
+        self.handle   = open(self.fileName, "w")
+        self.handle.write("track type=wiggle_0 name=\"%s\"\n" % (self.title))
+        for strand in self.data:
+            for chromosome in sorted(self.data[strand]):
+                 self.handle.write("variableStep chrom=%s%s\n" % (chromosome, strand2string[strand]))
+                 for pos in sorted(self.data[strand][chromosome]):
+                     self.handle.write("%d\t%d\n" % (pos, self.data[strand][chromosome][pos]))
+        self.handle.close()
+
+        
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["wig", "wiggle"]
+        
+        
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "wig"
+        
+        
+    def setTitle(self, title):
+        """
+        Set the title of the track
+        @param title: the title of the track
+        @type    title: string
+        """
+        if title != None:
+            self.title = title
+
+
+    def setStrands(self, strands):
+        """
+        Consider each strand separately
+        @param boolean: whether each strand should be considered separately
+        @type  boolean: boolean
+        """
+        self.strands = strands
+
+
+    def copyProperties(self, parser):
+        """
+        Copy the properties collected by a parser, to produce a similar output
+        @param bedParser: a parser
+        @type    bedParser: class L{TranscriptListWriter<TranscriptListWriter>}
+        """
+        self.setTitle(parser.title)
+        
+
+    def addTranscript(self, transcript):
+        """
+        Export the given transcript with GBrowse format
+        @param transcript: transcript to be printed
+        @type transcript: class L{Transcript<Transcript>}
+        @return: a string
+        """
+        chromosome = transcript.getChromosome()
+        direction  = transcript.getDirection()
+        if not self.strands:
+            direction = 0
+        if chromosome not in self.data[direction]:
+            self.data[direction][chromosome] = {}
+        for exon in transcript.getExons():
+            for pos in range(exon.getStart(), exon.getEnd()+1):
+                if pos not in self.data[direction][chromosome]:
+                    self.data[direction][chromosome][pos]  = 1
+                else:
+                    self.data[direction][chromosome][pos] += 1