diff commons/core/parsing/CoordsParser.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/CoordsParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,137 @@
+#
+# 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 re
+import sys
+from SMART.Java.Python.structure.Mapping import Mapping
+from commons.core.parsing.MapperParser import MapperParser
+from SMART.Java.Python.structure.SubMapping import SubMapping
+from SMART.Java.Python.misc import Utils
+
+class CoordsParser(MapperParser):
+    """A class that parses the .coords output of Nucmer"""
+
+    def __init__(self, fileName, verbosity = 0):
+        self._lineParseRe = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+\|\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
+        self._lineParseRe2 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
+        self._lineParseRe3 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+\|\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+\|\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+\|\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+\|\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
+        self._lineParseRe4 = re.compile(r"^\s*(?P<tStart>\d+)\s+(?P<tEnd>\d+)\s+(?P<qStart>\d+)\s+(?P<qEnd>\d+)\s+(?P<tLength>\d+)\s+(?P<qLength>\d+)\s+(?P<identity>\d+\.?\d*)\s+(?P<sim>\d+\.?\d*)\s+(?P<stp>\d+\.?\d*)\s+(?P<rlen>\d+\.?\d*)\s+(?P<qlen>\d+\.?\d*)\s+(?P<rcov>\d+\.?\d*)\s+(?P<qcov>\d+\.?\d*)\s+(?P<rframe>[-]?\d+\.?\d*)\s+(?P<qframe>[-]?\d+\.?\d*)\s+(?P<tName>[\w\|\:\-]+)\s+(?P<qName>.*)\s*$")
+        self.lineType = 1
+        MapperParser.__init__(self, fileName, verbosity)
+        
+    def getFileFormats():
+        return ["coords"]
+    getFileFormats = staticmethod(getFileFormats)
+
+    def skipFirstLines(self):    
+        while True: 
+            line = self.handle.readline()
+            self.currentLineNb += 1
+            if line == "":
+                break
+            if "=====" in line:
+                break
+            if "[S1]\t[E1]\t[S2]\t[E2]\t[LEN 1]\t[LEN 2]\t[% IDY]\t[LEN R]\t[LEN Q]\t[COV R]\t[COV Q]\t[FRM]\t[TAGS]" in line:
+                self.lineType = 2
+                break
+            if "[S1]     [E1]  |     [S2]     [E2]  |  [LEN 1]  [LEN 2]  |  [% IDY]  [% SIM]  [% STP]  | [FRM]  [TAGS]" in line:
+                self.lineType = 3
+           
+            if "[% IDY]\t[% SIM]\t[% STP]" in line and "[LEN Q]"in line:
+                self.lineType = 4 
+                break     
+        
+    def parseLine(self, line):
+        
+        if self.lineType == 1 : 
+            m = self._lineParseRe.search(line)
+        elif self.lineType == 2:
+            m = self._lineParseRe2.search(line)
+        elif self.lineType == 3:
+            m = self._lineParseRe3.search(line)
+        elif self.lineType == 4:
+            m = self._lineParseRe4.search(line)
+        if m == None:
+            sys.exit("\nLine %d '%s' does not have a NucMer format" % (self.currentLineNb, line))
+  
+        mapping = Mapping()
+        
+        subMapping = SubMapping()
+        subMapping.queryInterval.setName(m.group("qName"))
+        subMapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
+        subMapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
+        subMapping.queryInterval.setSize(int(m.group("qLength")))
+        subMapping.queryInterval.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
+        
+        subMapping.targetInterval.setChromosome(m.group("tName"))
+        subMapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
+        subMapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
+        subMapping.targetInterval.setSize(int(m.group("tLength")))
+        subMapping.targetInterval.setDirection(int(m.group("tEnd")) - int(m.group("tStart")))
+       
+        subMapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
+        subMapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
+        subMapping.setIdentity(float(m.group("identity")))
+        
+        mapping.addSubMapping(subMapping)
+        mapping.targetInterval.setStart(min(int(m.group("tStart")), int(m.group("tEnd"))))
+        mapping.targetInterval.setEnd(max(int(m.group("tStart")), int(m.group("tEnd"))))
+        mapping.targetInterval.setSize(int(m.group("tLength")))
+        mapping.targetInterval.setChromosome(m.group("tName"))
+         
+        mapping.queryInterval.setStart(min(int(m.group("qStart")), int(m.group("qEnd"))))
+        mapping.queryInterval.setEnd(max(int(m.group("qStart")), int(m.group("qEnd"))))
+        mapping.queryInterval.setSize(int(m.group("qLength")))
+        mapping.queryInterval.setName(m.group("qName"))
+        mapping.setDirection(int(m.group("qEnd")) - int(m.group("qStart")))
+        mapping.setSize(min(int(m.group("qLength")), int(m.group("tLength"))))
+        mapping.setIdentity(float(m.group("identity")))
+        mapping.setTagValue("feature", "match")
+        mapping.setTagValue("Target", "%s %d %d" % (m.group("qName"), int(m.group("qStart")), int(m.group("qEnd"))))
+                    
+        if self.lineType ==2 or self.lineType ==4:
+            mapping.setTagValue("target_pident", float(m.group("identity")))
+            mapping.setTagValue("target_pcover", float(m.group("qcov")))
+            mapping.setTagValue("target_length", int(m.group("qlen")))
+            
+        
+# Specific to Mark Work. Commented lines because of possible slowdown.                 
+#        for line in self.handle:
+#            string1 = line.strip()
+#            self.currentLineNb += 1
+#            break
+#        for line in self.handle:
+#            string2 = line.strip()
+#            self.currentLineNb += 1
+#            break
+#        print(len(string1),len(string2))
+#        mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
+        mapping.setNbGaps(0)
+
+        return mapping