diff TEisotools-1.1.a/commons/core/coord/MatchUtils.py @ 13:feef9a0db09d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/TEisotools-1.1.a/commons/core/coord/MatchUtils.py	Wed Jul 20 09:04:42 2016 -0400
@@ -0,0 +1,316 @@
+# Copyright INRA (Institut National de la Recherche Agronomique)
+# http://www.inra.fr
+# http://urgi.versailles.inra.fr
+#
+# 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 sys
+import math
+from commons.core.coord.Match import Match
+from commons.core.utils.FileUtils import FileUtils
+from commons.core.checker.RepetException import RepetException
+
+# # Static methods for the manipulation of Match instances
+#
+class MatchUtils (object):
+
+    # # Return a list with Match instances from the given file
+    #
+    # @param inFile name of a file in the Match format
+    # @return a list of Match instances
+    #
+    @staticmethod
+    def getMatchListFromFile(inFile):
+        lMatchInstances = []
+        inFileHandler = open(inFile, "r")
+        while True:
+            line = inFileHandler.readline()
+            if line == "":
+                break
+            if line[0:10] == "query.name":
+                continue
+            m = Match()
+            m.setFromString(line)
+            lMatchInstances.append(m)
+        inFileHandler.close()
+        return lMatchInstances
+
+    # #  Split a Match list in several Match lists according to the subject
+    #
+    #  @param lMatches a list of Match instances
+    #  @return a dictionary which keys are subject names and values Match lists
+    #
+    @staticmethod
+    def getDictOfListsWithSubjectAsKey(lMatches):
+        dSubject2MatchList = {}
+        for iMatch in lMatches:
+            if not dSubject2MatchList.has_key(iMatch.range_subject.seqname):
+                dSubject2MatchList[ iMatch.range_subject.seqname ] = []
+            dSubject2MatchList[ iMatch.range_subject.seqname ].append(iMatch)
+        return dSubject2MatchList
+
+    # #  Split a Match list in several Match lists according to the query
+    #
+    #  @param lMatches a list of Match instances
+    #  @return a dictionary which keys are query names and values Match lists
+    #
+    @staticmethod
+    def getDictOfListsWithQueryAsKey (lMatches):
+        dQuery2MatchList = {}
+        for iMatch in lMatches:
+            if not dQuery2MatchList.has_key(iMatch.range_query.seqname):
+                dQuery2MatchList[ iMatch.range_query.seqname ] = []
+            dQuery2MatchList[ iMatch.range_query.seqname ].append(iMatch)
+        return dQuery2MatchList
+
+    # # Write Match instances contained in the given list
+    #
+    # @param lMatches a list of Match instances
+    # @param fileName name of the file to write the Match instances
+    # @param mode the open mode of the file ""w"" or ""a""
+    #
+    @staticmethod
+    def writeListInFile(lMatches, fileName, mode = "w", header = None):
+        fileHandler = open(fileName, mode)
+        if header:
+            fileHandler.write(header)
+        for iMatch in lMatches:
+            iMatch.write(fileHandler)
+        fileHandler.close()
+
+    # # Give path id list from a list of Match instances
+    #
+    # @param lMatch list of Match instances
+    # @return lId integer list
+    #
+    @staticmethod
+    def getIdListFromMatchList(lMatch):
+        lId = []
+        for iMatch in lMatch:
+            lId.append(iMatch.id)
+        return lId
+
+    # # Remove duplicated matches in a match list
+    # ## replace old PyRepet.MatchDB.rmvDoublons()
+    #
+    # @param lMatch list of Match instances
+    # @return lMatchesUniq match unique list
+    #
+    @staticmethod
+    def rmvDuplicateMatches(lMatch):
+        lMatchesUniq = []
+        for match in lMatch:
+            if len(lMatchesUniq) == 0:
+                lMatchesUniq.append(match)
+            else:
+                nbDoublons = 0
+                for m in lMatchesUniq:
+                    if match.isDoublonWith(m):
+                        nbDoublons += 1
+                if nbDoublons == 0:
+                    lMatchesUniq.append(match)
+
+        for match1 in lMatchesUniq:
+            for match2 in lMatchesUniq:
+                if match1.id != match2.id:
+                    if match1.isDoublonWith(match2):
+                        raise RepetException ("*** Error: doublon not removed")
+        return lMatchesUniq
+
+    # # Return the list of queries 'included' in subjects when two different databanks are used.
+    # #replace old pyRepet.MatchDB.filterDiffQrySbj()
+    #
+    # @param iBioseqDB bioseqDB databank of queries
+    # @param thresIdentity float identity threshold
+    # @param thresLength float length threshold
+    # @param verbose int verbosity
+    #
+    # @return lMatches match list to keep according to length and identity thresholds
+    # TODO: don't take into account match for sequence against itself. To do ?
+    @staticmethod
+    def filterDiffQrySbj(iBioseqDB, matchFile, thresIdentity = 0.95, thresLength = 0.98, verbose = 0):
+        if verbose > 0:
+            print "filtering matches (id>=%.2f,qlgth>=%.2f)..." % (thresIdentity, thresLength); sys.stdout.flush()
+
+        thresIdentityPerc = math.floor(thresIdentity * 100)
+        lQryToKeep = []
+        dQry2Matches = MatchUtils.getDictOfListsWithQueryAsKey(MatchUtils.getMatchListFromFile(matchFile))
+
+        for seqH in iBioseqDB.idx.keys():
+            # keep it if it has no match
+            if not dQry2Matches.has_key(seqH):
+                if seqH not in lQryToKeep:
+                    lQryToKeep.append(seqH)
+            else:
+                isConditionsMet = False
+                for match in dQry2Matches[ seqH ]:
+                    # check if they are above the thresholds
+                    if match.identity >= thresIdentityPerc and match.query_length_perc >= thresLength:
+                        isConditionsMet = True
+                        break
+                if not isConditionsMet and  seqH not in lQryToKeep:
+                    lQryToKeep.append(seqH)
+        return lQryToKeep
+
+    # # Count the number of distinct matches involved in at least one match above the thresholds.
+    # #replace old pyRepet.coord.MatchDB.getNbDistinctSbjWithThres() and pyRepet.coord.MatchDB.getNbDistinctSbjWithThres()
+    #
+    # @param thresIdentity float identity threshold
+    # @param thresLength float length threshold
+    #
+    @staticmethod
+    def getNbDistinctSequencesInsideMatchesWithThresh(lMatches, thresIdentity = 0.95, thresLength = 0.98, whatToCount = "query"):
+        thresIdentityPerc = math.floor(thresIdentity * 100)
+        countSbj = 0
+        if whatToCount.lower() == "query":
+            dMatches = MatchUtils.getDictOfListsWithQueryAsKey(lMatches)
+        else:
+            dMatches = MatchUtils.getDictOfListsWithSubjectAsKey(lMatches)
+
+        for qry in dMatches.keys():
+            countMatch = 0
+            for match in dMatches[ qry ]:
+
+                if match.identity >= thresIdentityPerc and getattr(match, whatToCount.lower() + "_length_perc") >= thresLength:
+                    countMatch += 1
+            if countMatch > 0:
+                countSbj += 1
+        return countSbj
+
+    # # Convert a 'match' file (output from Matcher) into an 'align' file
+    # # replace old parser.tab2align
+    #
+    # @param inFileName  a string input file name
+    #
+    @staticmethod
+    def convertMatchFileToAlignFile(inFileName):
+        basename = os.path.splitext(inFileName)[0]
+        outFileName = "%s.align" % basename
+        outFile = open(outFileName, "w")
+
+        lMatches = MatchUtils.getMatchListFromFile(inFileName)
+
+        for match in lMatches:
+            string = "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (match.getQueryName(), match.getQueryStart(), match.getQueryEnd(), match.getSubjectName(), match.getSubjectStart(), match.getSubjectEnd(), match.getEvalue(), match.getScore(), match.getIdentity())
+            outFile.write(string)
+
+        outFile.close()
+
+    # # Convert a 'match' file (output from Matcher) into an 'abc' file (MCL input file)
+    # for each match, compute coverage on the smallest seq using this expression
+    #           Min (|QMatchEnd - QMatchStart + 1|,|SMatchEnd - SMatchStart + 1|)
+    #coverage = -----------------------------------------------------------------
+    #                             Min (QLength,SLength)
+    #
+    # Use this coverage for arc value. Matches of a sequence on itself are filtered.
+    #
+    # @param matchFileName string input match file name
+    # @param outFileName string output abc file name
+    # @param coverage float coverage filter threshold
+    #
+    @staticmethod
+    def convertMatchFileIntoABCFileWithCoverageComputeOnSmallestSeq(matchFileName, outFileName, coverageThreshold = 0):
+        sSeqNames = set()
+        sSeqNamesUsed = set()
+        with open(outFileName, "w") as outF:
+            with open(matchFileName) as inF:
+                inF.readline()
+                for inLine in inF:
+                    splittedLine = inLine.split("\t")
+                    qName = splittedLine[0]
+                    sName = splittedLine[6]
+                    sSeqNames.add(qName)
+                    sSeqNames.add(sName)
+                    if qName != sName:
+                        matchMin = min(abs(float(splittedLine[2]) - float(splittedLine[1]) + 1), abs(float(splittedLine[8]) - float(splittedLine[7]) + 1))
+                        seqMin = min(int(splittedLine[3]) / float(splittedLine[4]), int(splittedLine[9]) / float(splittedLine[10]))
+                        coverage = round(matchMin / seqMin, 2)
+                        if coverage >= coverageThreshold:
+                            outF.write("%s\n" % "\t".join([qName, sName, str(coverage)]))
+                            sSeqNamesUsed.add(qName)
+                            sSeqNamesUsed.add(sName)
+
+        with open("%s.unused" % outFileName, "w") as outSeqNameOfUnusedMatchesF:
+            for seqName in sorted(sSeqNames - sSeqNamesUsed):
+                outSeqNameOfUnusedMatchesF.write("%s\n" % seqName)
+
+        if FileUtils.isEmpty(outFileName):
+            print "WARNING: '%s' is empty." % outFileName
+
+    # # Convert a 'match' file (output from Matcher) into an 'abc' file (MCL input file)
+    # Use coverage on query for arc value
+    #
+    # @param matchFileName string input match file name
+    # @param outFileName string output abc file name
+    # @param coverage float query coverage filter threshold
+    #
+    @staticmethod
+    def convertMatchFileIntoABCFileOnQueryCoverage(matchFileName, outFileName, coverage = 0):
+        with open(matchFileName) as inF:
+                with open(outFileName, "w") as outF:
+                    inF.readline()
+                    for inLine in inF:
+                        splittedLine = inLine.split("\t")
+                        if float(splittedLine[4]) >= coverage:
+                            outLine = "\t".join([splittedLine[0], splittedLine[6], splittedLine[4]])
+                            outLine += "\n"
+                            outF.write(outLine)
+
+        if FileUtils.isEmpty(outFileName):
+            print "WARNING: '%s' is empty." % outFileName
+
+    # # Adapt the path IDs as the input file is the concatenation of several 'Match' files, and remove the extra header lines.
+    # # replace old parser.tabnum2id
+    #
+    # @param fileName  a string input file name
+    # @param  outputFileName  a string output file name (optional)
+    #
+    @staticmethod
+    def generateMatchFileWithNewPathId(fileName, outputFileName = None):
+        if outputFileName is None:
+            outFile = open(fileName, "w")
+        else:
+            outFile = open(outputFileName, "w")
+        outFile.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n")
+
+        lMatches = MatchUtils.getMatchListFromFile(fileName)
+        count = 1
+        dMatchKeyIdcount = {}
+
+        for match in lMatches:
+            key_id = str(match.getIdentifier()) + "-" + match.getQueryName() + "-" + match.getSubjectName()
+            if not key_id in dMatchKeyIdcount.keys():
+                newPath = count
+                count += 1
+                dMatchKeyIdcount[ key_id ] = newPath
+            else:
+                newPath = dMatchKeyIdcount[ key_id ]
+
+            match.id = newPath
+            outFile.write(match.toString() + "\n")
+        outFile.close()