class RNA(Polynucleotide):
alphabet_dict = {'strict':IUPACUnambiguousRNA(),'permissive':IUPACAmbiguousRNA()}
def get_dna(self,*args,**kwargs):
return self.convert_sequence(*args,**kwargs).back_transcribe()
def get_rna(self,*args,**kwargs):
return self.convert_sequence(*args,**kwargs)
def get_protein(self,*args,**kwargs):
return self.translate(*args,**kwargs)
def seqcategory(oneseq):
seqtype=''
seqDNA=Seq(oneseq,IUPACAmbiguousDNA()) #Produce a sequence using the string received and the DNA alphabet.
seqRNA=Seq(oneseq,IUPACAmbiguousRNA()) #Produce a sequence using the string received and the RNA alphabet.
seqProt=Seq(oneseq,ExtendedIUPACProtein()) #Produce a sequence using the string received and the protein alphabet.
if Alphabet._verify_alphabet(seqDNA): #Verify if is a DNA sequence.
seqtype='DNA'
elif Alphabet._verify_alphabet(seqRNA): #Verify if is a RNA sequence.
seqtype='RNA'
else:
if Alphabet._verify_alphabet(seqProt): #Verify if is a protein sequence.
seqtype='protein'
else:
seqtype='noseq' #If any, is not a valid sequence.
return seqtype
parser.add_argument('-pw',
'--pwa-width',
type=int,
default='60',
help='pairwise alignment output width')
args = parser.parse_args()
for file in (args.query_seq, args.target_seq):
if not path.isfile(file):
parser.error("File %s doesn't exist" % file)
# alphabet
if args.seq_type == 'dna':
args.seq_abc = IUPACAmbiguousDNA()
elif args.seq_type == 'rna':
args.seq_abc = IUPACAmbiguousRNA()
else:
args.seq_abc = ExtendedIUPACProtein()
# Aligners setup
aligners = {'global': PairwiseAligner(), 'local': None}
aligners['global'].mode = 'global'
if args.seq_type in ('dna', 'rna'):
aligners['global'].match = args.match_score
aligners['global'].mismatch = args.mismatch_score
if not args.open_gap_score:
args.open_gap_score = -5
if not args.extend_gap_score:
args.extend_gap_score = -2
else:
sub_matrix = getattr(import_module('Bio.SubsMat.MatrixInfo'),