def main():
(opts, args) = getoptions()
# Load PWMs
pssms = load_motifs(opts.pwm_dir, opts.pseudocount)
if opts.testseq is not None:
if opts.seqtype == 'RNA':
seq = Seq(opts.testseq,
IUPAC.IUPACUnambiguousRNA()).back_transcribe()
seq.alphabet = IUPAC.IUPACUnambiguousDNA()
else:
seq = Seq(opts.testseq, IUPAC.IUPACUnambiguousDNA())
final = scan_all(pssms, seq, opts)
print final.to_csv(sep="\t", index=False)
else:
# Scan in sequence
print >> sys.stderr, "Scanning sequences ",
tic = time.time()
for seqrecord in SeqIO.parse(open(args[0]), "fasta"):
seq = seqrecord.seq
if opts.seqtype == "RNA":
seq = seq.back_transcribe()
seq.alphabet = IUPAC.IUPACUnambiguousDNA()
final = scan_all(pssms, seq, opts)
print final.to_csv(sep="\t", index=False)
toc = time.time()
print >> sys.stderr, "done in %0.2f seconds!" % (float(toc - tic))
def main(): (opts, args) = getoptions() # Load PWMs pssms = load_motifs(opts.pwm_dir, opts.pseudocount) if opts.testseq is not None: if opts.seqtype == 'RNA': seq = Seq(opts.testseq, IUPAC.IUPACUnambiguousRNA()).back_transcribe() seq.alphabet = IUPAC.IUPACUnambiguousDNA() else: seq = Seq(opts.testseq, IUPAC.IUPACUnambiguousDNA()) final = scan_all(pssms, seq, opts) print final.to_csv(sep="\t", index = False) else: # Scan in sequence print >> sys.stderr, "Scanning sequences ", tic = time.time() for seqrecord in SeqIO.parse(open(args[0]), "fasta"): seq = seqrecord.seq if opts.seqtype == "RNA": seq = seq.back_transcribe() seq.alphabet = IUPAC.IUPACUnambiguousDNA() final = scan_all(pssms, seq, opts) print final.to_csv(sep="\t", index = False) toc = time.time() print >> sys.stderr, "done in %0.2f seconds!" % (float(toc - tic))
def ConcatenatingSeq():
protein_seq = Seq("EVRNAK", IUPAC.protein)
dna_seq = Seq("ACGT", IUPAC.unambiguous_dna)
#print(protein_seq + dna_seq) #error
protein_seq.alphabet = generic_alphabet
dna_seq.alphabet = generic_alphabet
print(protein_seq + dna_seq)
list_of_seqs = [
Seq("ACGT", generic_dna),
Seq("AACC", generic_dna),
Seq("GGTT", generic_dna)
]
concatenated = Seq("", generic_dna)
for s in list_of_seqs:
concatenated += s
print('concatenated=', concatenated)
con = sum(list_of_seqs, Seq("", generic_dna))
print('con=', con)
dna_seq = Seq("acgtACGT", generic_dna)
print('unper=', dna_seq.upper())
print('lower=', dna_seq.lower())
print("GTAC" in dna_seq)
print("GTAC" in dna_seq.upper())
def translate(self):
seq = self.seq()
try:
seq = Seq(seq.tostring()[self.frame:], self.alphabet)
except TypeError:
seq.alphabet = self.alphabet
try:
return seq.translate() #default table
except AssertionError:
# if the feature was pickled then we have problems
import cPickle
if cPickle.dumps(seq.alphabet) == cPickle.dumps(DEFAULT_ALPHABET):
seq.alphabet = DEFAULT_ALPHABET
return seq.translate()
else:
raise
def translate(self):
seq = self.seq()
try:
seq = Seq(seq.tostring()[self.frame:], self.alphabet)
except TypeError:
seq.alphabet = self.alphabet
try:
return standard_translator.translate(seq)
except AssertionError:
# if the feature was pickled then we have problems
import cPickle
if cPickle.dumps(seq.alphabet) == cPickle.dumps(DEFAULT_ALPHABET):
seq.alphabet = DEFAULT_ALPHABET
return standard_translator.translate(seq)
else:
raise
def cre (*args):
in_srecs = []
for arg in args:
in_srecs += decre (arg)
seen_seqs = {}
index_list = []
for i in xrange (len (in_srecs)):
k = str (in_srecs[i].seq)
if not seen_seqs.has_key (k):
seen_seqs[k] = i
index_list.append (seen_seqs[k])
out_srecs = []
for p in circular_permutations (index_list):
s = Seq ("")
names = []
i = 0
for index in p:
srec = in_srecs[index]
i += 1
s += srec.seq
name = srec.annotations.get (CREACEMBLER_TAG, None)
if not name:
name = "seq%02d" % (i,)
names.append (name)
s.alphabet = generic_dna
combined_srec = SeqRecord (s)
combined_srec.annotations[CREACEMBLER_TAG] = "_x_".join (names)
out_srecs.append (combined_srec)
return out_srecs
def decre (srec): n_fwd = srec.seq.upper ().count (LOXPFWD) n_rev = srec.seq.upper ().count (LOXPREV) if n_fwd > 0 and n_rev > 0: raise FwdAndRevLoxSite (srec) need_revcomp = False if n_fwd > 0: sep = LOXPFWD elif n_rev > 0: sep = LOXPREV need_revcomp = True else: raise NoLoxSite (srec) out = [] original_name = srec.annotations.get (CREACEMBLER_TAG, "seq") count = 0 parts = srec.seq.upper ().split (sep) parts[-1] += parts[0] parts = parts[1:] for p in parts: count += 1 if need_revcomp: p = p.reverse_complement () s = Seq (LOXPFWD) + p s.alphabet = generic_dna srec = SeqRecord (s) if len (parts) > 1: name = "%s%02d" % (original_name, count) else: name = original_name srec.annotations[CREACEMBLER_TAG] = name out.append (srec) return out
str(my_seq)
print(my_seq)
fasta_format_string = ">Name\n%s\n" % my_seq
print(fasta_format_string)
# Concatenating or adding sequences
from Bio.Alphabet import IUPAC
from Bio.Seq import Seq
protein_seq = Seq("EVRNAK", IUPAC.protein)
dna_seq = Seq("ACGT", IUPAC.unambiguous_dna)
#protein_seq + dna_seq
## Error expected
from Bio.Alphabet import generic_alphabet
protein_seq.alphabet = generic_alphabet
dna_seq.alphabet = generic_alphabet
protein_seq + dna_seq
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
list_of_seqs = [Seq("ACGT", generic_dna), Seq("AACC", generic_dna), Seq("GGTT", generic_dna)]
sum(list_of_seqs, Seq("", generic_dna))
# Changing case
from Bio.Seq import Seq
from Bio.Alphabet import generic_dna
dna_seq = Seq("acgtACGT", generic_dna)
dna_seq
dna_seq.upper()
print(str(my_seq))
fasta_format_string = ">Name\n%s\n" % my_seq
print(fasta_format_string)
#print(my_seq.tostring())
#序列连接
protein_seq = Seq("EVRNAK", IUPAC.protein)
dna_seq = Seq("ACGT", IUPAC.unambiguous_dna)
try:
print(protein_seq + dna_seq)
except:
print("字母表不兼容，连接失败！")
#字母表转换为兼容类型
from Bio.Alphabet import generic_alphabet
protein_seq.alphabet = generic_alphabet
dna_seq.alphabet = generic_alphabet
try:
print(protein_seq + "--" + dna_seq)
print("字母表兼容，连接成功！")
except:
print("字母表不兼容，连接失败！")
#连接后字母表的变化
from Bio.Alphabet import generic_nucleotide
nuc_seq = Seq("GATCGATGC", generic_nucleotide)
dna_seq = Seq("ACGT", IUPAC.unambiguous_dna)
print(nuc_seq.alphabet, "+", dna_seq.alphabet, "=", (nuc_seq + dna_seq).alphabet)
#大小写更改
#!/usr/bin/python
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
seq = raw_input("enter your sequence: ")
my_s = Seq(seq)
print my_s
my_s.alphabet()
s2 = Seq('ACGTACGTACGTACGT', IUPAC.IUPACAmbiguousDNA())
try:
assert (isinstance (IUPAC.Alphabet._get_base_alphabet(s2.alphabet), IUPAC.ExtendedIUPACDNA))
except AssertionError:
print "wrong type"
isinstance (IUPAC.Alphabet._get_base_alphabet(s2.alphabet), IUPAC.ExtendedIUPACDNA)
#>>> False
my_seq = Seq(seq, IUPAC.extended_dna)
print "original\t\t", my_seq
print "complement\t\t", my_seq.complement()
print "reverse_complement\t", my_seq.reverse_complement()
import Bio
from Bio.Seq import Seq
print(Bio._Version_)
my_sequence = Seq('AGTATACTATGTGCATAGTCAGTCAGTCGA')
print(my_sequence)
print(my_sequence.alphabet())
my_sequence_complement = my_sequence.complement()
print(my_sequence_complement)
parser.add_argument("--max_primers_to_return", type=int, default=5)
args = parser.parse_args()
slop = args.slop
alphabet = Alphabet()
alphabet.letters = ["A", "T", "C", "G", "[", "]"]
with open(args.flagged, "w") as fh:
for seq_record in SeqIO.parse(args.fasta, "fasta"):
if args.primer3:
sequence = str(seq_record.seq)
fh.write("SEQUENCE_ID=%s\n" % seq_record.id)
fh.write("SEQUENCE_TEMPLATE=%s\n" % sequence)
fh.write("SEQUENCE_TARGET=%i,%i\n" % (slop, len(sequence) - 2 * slop))
fh.write("PRIMER_OPT_SIZE=%i\n" % args.opt_primer_size)
fh.write("PRIMER_MIN_SIZE=%i\n" % args.min_primer_size)
fh.write("PRIMER_MAX_SIZE=%i\n" % args.max_primer_size)
fh.write("PRIMER_NUM_RETURN=%i\n" % args.max_primers_to_return)
fh.write("=\n")
else:
sequence = Seq(
str(seq_record.seq)[:slop]
+ "["
+ str(seq_record.seq)[slop:-slop]
+ "]"
+ str(seq_record.seq)[-slop:]
)
sequence.alphabet = alphabet
flagged_seq_record = SeqRecord(sequence, id=seq_record.id, description="")
SeqIO.write([flagged_seq_record], fh, "fasta")
print myseq.count('aa') #must use same capitalize, non overlapping
print GC(myseq) # GC content
print myseq[2:10] #the slice is a new Seq with same alphabet
myseq2 = myseq[::3]
print myseq2, myseq2.alphabet
print myseq[::-1]
print str(myseq), type(str(myseq)) # (automatic) convert to string
#Concatenating sequences
protseq = Seq('EVRNAK',IUPAC.protein)
dnaseq = Seq('ACGT',IUPAC.unambiguous_dna)
#print protseq+dnaseq #can't concatenate seqs with different alphabets
print myseq+dnaseq
from Bio.Alphabet import generic_alphabet
protseq.alphabet = generic_alphabet # in order to concatenate them
dnaseq.alphabet = generic_alphabet # must use generic_alphabet
print protseq+dnaseq
from Bio.Alphabet import generic_nucleotide
nucseq = Seq('GATCGATGC',generic_nucleotide)
dnaseq = Seq('ACGT',IUPAC.unambiguous_dna)
print nucseq.alphabet, dnaseq.alphabet
print nucseq + dnaseq, (nucseq + dnaseq).alphabet # parent + child = parent type
from Bio.Alphabet import generic_dna
list_seqs = [Seq('ACGT', generic_dna), Seq('CCGG', generic_dna), Seq('TTATT', generic_dna)]
concatenated = Seq('',generic_dna)
for seq in list_seqs:
concatenated += seq
print concatenated
from Bio.Alphabet import IUPAC, generic_alphabet
from Bio.Seq import Seq
dna = Seq("ATGGTTAGTCTTTAA", IUPAC.unambiguous_dna)
protein = dna.translate()
#try to concetenate dna and protein sequences
try:
concetencate = dna + protein
print("Contenated successfully")
#this attempt has been failed because dna and protein use different alphabet.
except:
#we need same types to concetenate.
dna.alphabet = generic_alphabet
protein.alphabet = generic_alphabet
print(dna + protein)
