def getSetListFromQuery(self, query):
lpath = self.getPathListFromQuery(query)
lSet = PathUtils.getSetListFromQueries(lpath)
return lSet
def getSetListIncludedInQueryCoord(self, query, start, end):
lPath=self.getPathListIncludedInQueryCoord(query, start, end)
lSet = PathUtils.getSetListFromQueries(lPath)
return lSet
else:
print "ERROR: unknown subject table type: %s" % ( stype )
sys.exit(1)
lSetIdToRemovePaths = []
count = 0
# for each path ID
for id in lPathId:
string = "processing path '%i'..." % ( id )
if qtype == "path":
lPaths = qtablePathAdaptator.getPathListFromId( id )
lQuerySets = PathUtils.getSetListFromQueries( lPaths )
elif qtype == "set":
lQuerySets = qtableSetAdaptator.getSetListFromId( id )
lQuerySets.sort()
qmin, qmax = SetUtils.getListBoundaries( lQuerySets )
qmin = qmin - 1
qmax = qmax + 1
if stype == "path":
lPaths = stablePathAdaptator.getPathListOverlappingQueryCoord( lQuerySets[0].seqname.split()[0], qmin, qmax )
lSubjectSets = PathUtils.getSetListFromQueries( lPaths )
elif stype == "set":
lSubjectSets = stableSetAdaptator.getSetListFromQueryCoord( lQuerySets[0].seqname.split()[0], qmin, qmax )
if verbose > 1:
def getSetListOverlappingQueryCoord(self, query, start, end):
lPath = self.getPathListOverlappingQueryCoord(query, start, end)
lSet = PathUtils.getSetListFromQueries(lPath)
return lSet
if not os.path.exists( inFileName ):
msg = "ERROR: can't find file '%s'" % ( inFileName )
sys.stderr.write( "%s\n" % msg )
help()
sys.exit(1)
if outFileName == "":
outFileName = "%s.gff3" % ( inFileName )
if verbose > 0:
msg = "START %s" % ( sys.argv[0].split("/")[-1] )
msg += "\ninput file: %s" % ( inFileName )
msg += "\nsource: %s" % ( source )
msg += "\noutput file: %s" % ( outFileName )
sys.stdout.write( "%s\n" % msg )
sys.stdout.flush()
PathUtils.convertPathFileIntoGffFile( pathFile=inFileName,
gffFile=outFileName,
source=source,
verbose=verbose )
if verbose > 0:
print "END %s" % ( sys.argv[0].split("/")[-1] )
sys.stdout.flush()
return 0
if __name__ == "__main__":
main()
