test.py

from cogent.align.algorithm import nw_align as nw_align_cogent
from skbio.alignment import global_pairwise_align_nucleotide as nw_align_scikit


seq_1 = 'ATCGATCGATCG'
seq_2 = 'ATCGATATCGATCG'

print "Sequences: "
print "     %s" % seq_1
print "     %s" % seq_2
print

alignment = nw_align_scikit(seq_1, seq_2)
al_1, al_2 = [alignment.get_seq(_id).__str__() for _id in alignment.ids()]

print "    nw alignment using scikit:"
print "        %s" % al_1
print "        %s" % al_2
print

al_1, al_2 = nw_align_cogent(seq_1, seq_2)

print "    nw alignment using cogent:"
print "        %s" % al_1
print "        %s" % al_2
print


#    meren ~ $ python -W ignore test.py
#    Sequences:
#         ATCGATCGATCG
#         ATCGATATCGATCG
#
#         nw alignment using scikit:
#            ------ATCGATCGATCG
#            ATCGATATCGATCG----
#
#        nw alignment using cogent:
#            ATCGAT--CGATCG
#            ATCGATATCGATCG
#