class Match( Path ):
## Constructor
#
def __init__(self):
Path.__init__(self)
self.query_length = -1
self.query_length_perc = -1 # length of the match on the query / length of the query
self.query_seqlength = -1
self.match_length_perc = -1 # length of the match on the query / total length of the subject
self.subject_length = -1
self.subject_length_perc = -1 # length of the match on the subject / length of the subject
self.subject_seqlength = -1
## Equal operator
#
def __eq__(self, o):
if self.query_length != o.query_length or self.query_length_perc != o.query_length_perc\
or self.query_seqlength != o.query_seqlength or self.subject_length != o.subject_length\
or self.subject_length_perc != o.subject_length_perc or self.subject_seqlength != o.subject_seqlength\
or self.match_length_perc != o.match_length_perc:
return False
else:
return Path.__eq__(self, o)
## Return the length of the match on the query divided by the total length of the query
#
def getLengthPercOnQuery(self):
return self.query_length_perc
## Return the length of the match on the subject divided by the total length of the subject
#
def getLengthPercOnSubject(self):
return self.subject_length_perc
## Return the length of the match on the subject
#
def getLengthMatchOnSubject(self):
return self.subject_length
## Set attributes from a tuple
#
# @param tuple: a tuple with (query name,query start,query end,
# query length, query length perc (between 0-1), match length perc (between 0-1), subject name,
# subject start,subject end,subject length, subject length percentage (between 0-1), e_value,score,identity,id)
#
def setFromTuple( self, tuple ):
queryStart = int(tuple[1])
queryEnd = int(tuple[2])
subjectStart = int(tuple[7])
subjectEnd = int(tuple[8])
if queryStart < queryEnd:
self.range_query = Range(tuple[0],queryStart,queryEnd)
self.range_subject = Range(tuple[6],subjectStart,subjectEnd)
else:
self.range_query = Range(tuple[0],queryEnd,queryStart)
self.range_subject = Range(tuple[6],subjectEnd,subjectStart)
self.query_length = int(tuple[3])
self.query_length_perc = float(tuple[4])
self.query_seqlength = int( self.query_length / self.query_length_perc )
self.match_length_perc = float(tuple[5])
self.subject_length = int(tuple[9])
self.subject_length_perc = float(tuple[10])
self.subject_seqlength = int( self.subject_length / self.subject_length_perc )
self.e_value = float(tuple[11])
self.score = float(tuple[12])
self.identity = float(tuple[13])
self.id = int(tuple[14])
## Reset
#
def reset( self ):
Path.reset( self )
self.query_length = -1
self.query_length_perc = -1
self.query_seqlength = -1
self.match_length_perc = -1
self.subject_length = -1
self.subject_length_perc = -1
self.subject_seqlength = -1
## Return a formated string of the attribute data
#
def toString( self ):
string = "%s" % ( self.range_query.toString() )
string += "\t%i\t%f" % ( self.query_length,
self.query_length_perc )
string += "\t%f" % ( self.match_length_perc )
string += "\t%s" % ( self.range_subject.toString() )
string += "\t%i\t%f" % ( self.subject_length,
self.subject_length_perc )
string += "\t%g\t%i\t%f" % ( self.e_value,
self.score,
self.identity )
string += "\t%i" % ( self.id )
return string
## Return a Path instance
#
def getPathInstance( self ):
p = Path()
tuple = ( self.id,
self.range_query.seqname,
self.range_query.start,
self.range_query.end,
self.range_subject.seqname,
self.range_subject.start,
self.range_subject.end,
self.e_value,
self.score,
self.identity )
p.setFromTuple( tuple )
return p
## Give information about a match whose query is included in the subject
#
# @return string
#
def getQryIsIncluded( self ):
string = "query %s (%d bp: %d-%d) is contained in subject %s (%d bp: %d-%d): id=%.2f - %.3f - %.3f - %.3f" %\
( self.range_query.seqname, self.query_seqlength, self.range_query.start, self.range_query.end,
self.range_subject.seqname, self.subject_seqlength, self.range_subject.start, self.range_subject.end,
self.identity, self.query_length_perc, self.match_length_perc, self.subject_length_perc )
return string
## Compare the object with another match and see if they are equal
# (same identity, E-value and score + same subsequences whether in query or subject)
#
# @return True if objects are equals False otherwise
#
def isDoublonWith( self, match, verbose=0 ):
# if both matches have same identity, score and E-value
if self.identity == match.identity and self.score == match.score and self.e_value == match.e_value:
# if query and subject are identical
if ( self.range_query.seqname == match.range_query.seqname \
and self.range_subject.seqname == match.range_subject.seqname ):
# if the coordinates are equal
if self.range_query.__eq__( match.range_query ) and self.range_subject.__eq__( match.range_subject ):
return True
else:
if verbose > 0: print "different coordinates"; sys.stdout.flush()
return False
# if query and subject are reversed but identical
elif self.range_query.seqname == match.range_subject.seqname and self.range_subject.seqname == match.range_query.seqname:
# if the coordinates are equal
if self.range_query.__eq__( match.range_subject ) and self.range_subject.__eq__( match.range_query ):
return True
else:
if verbose > 0: print "different coordinates"; sys.stdout.flush()
return False
else:
if verbose > 0: print "different sequence names"; sys.stdout.flush()
return False
else:
if verbose > 0: print "different match numbers"; sys.stdout.flush()
return False
def __eq__(self, o):
if self.name == o.name:
return Range.__eq__(self, o)
return False