Python align_unaligned_seqsの例

コード例 #1

ファイル: vcf_to_fasta.py プロジェクト: johnchase/wilder_lab

def create_2_base_sub(alleles, ref, alt): 
    bases_list = alt.split(', ')
    bases_list.insert(0, ref)
    seqs = [bases_list[alleles[0]], bases_list[alleles[1]]]  
    scaffold = max(bases_list, key=len)
    substitution = []
    for seq in seqs:
        if len(seq) == len(scaffold): 
            substitution.append(seq)
        elif seq == '.':
            substitution.append('-'*len(scaffold))
        else:
            seq_and_scaffold = [seq, scaffold]
            aligned_seqs = align_unaligned_seqs(seq_and_scaffold, DNA, params={'-gapopen': -0.001})
            aligned_seqs = str(aligned_seqs)
            bases_sub = aligned_seqs.split('\n')
            substitution.append(bases_sub[3])
    return substitution

コード例 #2

ファイル: BuildGeneTrees.py プロジェクト: kingsfordgroup/parana2

def main():
  fdir = sys.argv[1]
  odir = sys.argv[2]
  mkdir_p(odir)

  for fname in glob.iglob("{0}/*.fasta".format(fdir)):

    groupName = fname.split( os.path.sep )[-1].rstrip(".fasta")
    print("group {0}".format(groupName))
    try:
      seqs = cogent.LoadSeqs(fname, moltype=cogent.PROTEIN, aligned=False)
    except Exception as e:
      print(e)
      exit(0)
    aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
    t = build_tree_from_alignment(aln, cogent.PROTEIN)
    print("tree for group {0}".format( str(t) ) )
    with open( os.path.sep.join( [ odir, groupName+".nwk" ] ), 'wb') as ofile:
        ofile.write( str(t).replace("'","") )

コード例 #3

def main():
    fdir = sys.argv[1]
    odir = sys.argv[2]
    mkdir_p(odir)

    for fname in glob.iglob("{0}/*.fasta".format(fdir)):

        groupName = fname.split(os.path.sep)[-1].rstrip(".fasta")
        print("group {0}".format(groupName))
        try:
            seqs = cogent.LoadSeqs(fname,
                                   moltype=cogent.PROTEIN,
                                   aligned=False)
        except Exception as e:
            print(e)
            exit(0)
        aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
        t = build_tree_from_alignment(aln, cogent.PROTEIN)
        print("tree for group {0}".format(str(t)))
        with open(os.path.sep.join([odir, groupName + ".nwk"]), 'wb') as ofile:
            ofile.write(str(t).replace("'", ""))

コード例 #4

ファイル: BuildSingleTree.py プロジェクト: minye/parana2

def main():
    arguments = docopt(__doc__, version='BuildSingleTree v1.0')
    print(arguments)
    netname = arguments['<network>']
    seqname = arguments['<seqfile>']
    ofname = arguments['-o']

    print("creating tree for {0}".format(netname))
    print("using sequences from {0}".format(seqname))

    G = nx.read_adjlist(netname)
    try:
        seqs = cogent.LoadSeqs(seqname, moltype=cogent.PROTEIN, aligned=False)
    except Exception as e:
        print(e)
        sys.exit(0)

    aln = align_unaligned_seqs(seqs, cogent.PROTEIN)
    t = build_tree_From_alignment(aln, cogent.PROTEIN)
    print("tree  = {0}".format( str(t) ) )
    with open( os.path.sep.join( [ "all" ] ), 'wb') as ofile:
        ofile.write( str(t).replace("'","") )

コード例 #5

ファイル: test_muscle.py プロジェクト: carze/clovr-base

 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)

コード例 #6

 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)