1
2 """\
3 -------------------------------------------------------
4 fastaObservedDist.py
5 -------------------------------------------------------
6
7 fastaObservedDist.py [-h|--help] <fastafile>"
8
9 add length data on all sequences in the fasta file.
10
11 -------------------------------------------------------
12 -h --help : print this help
13 -------------------------------------------------------
14 """
15
16 import fileinput
17 import getopt
18
19 from obitools.fasta import fastaAligmentReader
20 from obitools.distances.observed import PairewiseGapRemoval
21 from obitools.distances.r import writeRMatrix
22 from obitools.utils import checkHelpOption
23
24
25
26 if __name__=='__main__':
27
28 checkHelpOption(__doc__)
29
30 ali = fastaAligmentReader(fileinput.input())
31 dist= PairewiseGapRemoval(ali)
32
33 print writeRMatrix(dist)
34