Example #1
0
 def __init__(self,out,lineLen=None,mode="w",compresslevel=6):
     if lineLen is None:
         lineLen = 1000
     if not hasattr(out,'write'):
         out = openCompressed(out,mode,compresslevel=compresslevel)
         self.outClose = True
     else:
         self.outClose = False
     self.out = out
     self.lineLen = lineLen
Example #2
0
 def __init__(self,infile):
     """Ctor.
     @param infile It can be either a string with a file name, or it can be an
     iterator that returns lines (each line should be terminated with a new line),
     e.g. a file object. An iterator can be a filter that reads another FastaReader
     object, performs transformations on the records and emits them as lines."""
     if is_string(infile):
         infile = openCompressed(infile,'r')
         self.ownInfile = True
     else:
         self.ownInfile = False
     self.infile = infile
     self.freshHdr = False
     self.maxLineLen = 0
     self.seqTotal = 0
     self.symbolsTotal = 0