diff commons/core/writer/CsvWriter.py @ 38:2c0c0a89fad7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/writer/CsvWriter.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,153 @@
+#
+# 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.
+#
+import os
+import random
+from commons.core.writer.TranscriptListWriter import TranscriptListWriter
+from SMART.Java.Python.misc.Progress import Progress
+
+class CsvWriter(TranscriptListWriter):
+    """
+    A class that writes a transcript list into a file with CSV (Excel) format
+    @ivar fileName: name of the file 
+    @type fileName: string
+    @ivar handle: handle to the file
+    @type handle: file handle
+    """
+
+
+    def __init__(self, fileName, verbosity = 0):
+        """
+        Constructor
+        @param fileName: name of the file 
+        @type fileName: string
+        @param verbosity: verbosity
+        @type verbosity: int
+        """
+        super(CsvWriter, self).__init__(fileName, verbosity)
+        self.header   = ""
+        self.title    = "chromosome,start,end,strand,exons,tags\n"
+        self.modified = False
+            
+
+    def __del__(self):
+        """
+        Destructor
+        (Trick to write 1 tag per column)
+        """
+        if self.handle != None:
+            self.modifyCsv()
+        super(CsvWriter, self).__del__()
+
+
+    def close(self):
+        if self.handle != None:
+            self.modifyCsv()
+        super(CsvWriter, self).close()
+
+
+    def modifyCsv(self):
+        """
+        Clean CSV file so that there is one column per tag
+        """
+        if self.modified:
+            return
+
+        # read all the tags
+        self.handle.close()
+        self.handle = open(self.fileName)
+        nbFirstFields = 5
+        tags = set()
+        if self.verbosity >= 10:
+            print "Modifying CSV file..."
+        number = -1
+        for number, line in enumerate(self.handle):
+            if number != 0:
+                theseTags = line.strip().split(",")[nbFirstFields:]
+                for tag in theseTags:
+                    if tag.find("=") != -1:
+                        (key, value) = tag.split("=", 1)
+                        if value != None:
+                            tags.add(key)
+        if self.verbosity >= 10:
+            print " ...done"
+
+        # re-write the file
+        tmpFileName = "tmpFile%d.csv" % (random.randint(0, 100000))
+        tmpFile = open(tmpFileName, "w")
+        self.handle.seek(0)
+        progress = Progress(number + 1, "Re-writting CSV file", self.verbosity)
+        tmpFile.write(self.title.replace("tags", ",".join(sorted(tags))))
+        for line in self.handle:
+            tagValues = dict([(key, None) for key in tags])
+            tmpFile.write(",".join(line.strip().split(",")[:nbFirstFields]))
+            for tag in line.strip().split(",")[nbFirstFields:]:
+                if tag.find("=") != -1:
+                    key = tag.split("=", 1)[0]
+                    tagValues[key] = tag.split("=", 1)[1]
+                else:
+                    tagValues[key] += ";%s" % (tag)
+            for key in sorted(tagValues.keys()):
+                tmpFile.write(",%s" % (tagValues[key]))
+            tmpFile.write("\n")
+            progress.inc()
+        tmpFile.close()
+
+        # replace former file
+        import shutil
+        shutil.move(tmpFile.name, self.fileName)
+        progress.done()
+        self.modified = True
+
+
+    @staticmethod
+    def getFileFormats():
+        """
+        Get the format of the file
+        """
+        return ["csv", "xls", "excel"]
+
+
+    @staticmethod
+    def getExtension():
+        """
+        Get the usual extension for the file
+        """
+        return "csv"
+        
+        
+    def printTranscript(self, transcript):
+        """
+        Export the given transcript with GFF2 format
+        @param transcript: transcript to be printed
+        @type transcript: class L{Transcript<Transcript>}
+        @return: a string
+        """
+        return transcript.printCsv()
+