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src/e/e/eebprogramming-HEAD/lec10review/8procs.py   eebprogramming(Download)
#!/usr/bin/env python
# taken from http://pycogent.sourceforge.net/
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.core.moltype import DNA
from cogent import LoadSeqs
from cogent.app.raxml import build_tree_from_alignment as raxml_build_tree
unaligned_seqs = LoadSeqs(filename='data/test2.fasta', aligned=False)
aln = mafft_align_unaligned_seqs(unaligned_seqs, DNA)

src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
 build_blast_db_from_fasta_path
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs
from cogent.parse.blast import BlastResult

src/c/o/cogent-1.5.3/tests/test_app/test_mafft.py   cogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.mafft import Mafft, align_unaligned_seqs, \
    add_seqs_to_alignment, align_two_alignments
 
    def test_align_unaligned_seqs(self):
        """align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), align1)
        res = align_unaligned_seqs(self.lines2, RNA)

src/p/y/pycogent-HEAD/tests/test_app/test_mafft.py   pycogent(Download)
from cogent.util.unit_test import TestCase, main
from cogent.util.misc import flatten
from cogent.app.mafft import Mafft, align_unaligned_seqs, \
    add_seqs_to_alignment, align_two_alignments
 
    def test_align_unaligned_seqs(self):
        """align_unaligned_seqs should work as expected"""
        res = align_unaligned_seqs(self.seqs1, RNA)
        self.assertEqual(res.toFasta(), align1)
        res = align_unaligned_seqs(self.lines2, RNA)

src/p/y/pynast-1.2.2/tests/test_util.py   pynast(Download)
from cogent.core.alignment import DenseAlignment
from cogent.app.muscle_v38 import align_unaligned_seqs as muscle_align_unaligned_seqs
from cogent.app.mafft import align_unaligned_seqs as mafft_align_unaligned_seqs
from cogent.app.clustalw import align_unaligned_seqs as clustal_align_unaligned_seqs
from cogent.parse.fasta import MinimalFastaParser