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from Bio import Seq
from Bio.Alphabet import IUPAC
from Bio import Alphabet
print
print "Testing Seq"
print "==========="
s = Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna)
print s.tostring()
print len(s)
print s[0]
print s[-1]
print s[3:5].tostring()
print "Reverse using -1 stride:", repr(s[::-1])
print "Extract every third nucleotide (slicing with stride 3):"
print repr(s[0::3])
print repr(s[1::3])
print repr(s[2::3])
print s.alphabet.letters
t = Seq.Seq("T", IUPAC.unambiguous_dna)
u = s + t
print str(u.alphabet)
print len(u)
assert s.tostring() + "T" == u.tostring()
t = Seq.Seq("T", IUPAC.protein)
try:
u = s + t
except TypeError:
print "expected error, and got it"
else:
print "huh? ERROR"
t = Seq.Seq("T", IUPAC.ambiguous_dna)
u = s + t
print str(u.alphabet)
from Bio.Seq import MutableSeq
import array
print
print "Testing MutableSeq"
print "=================="
print "Testing creating MutableSeqs in multiple ways"
string_seq = MutableSeq("TCAAAAGGATGCATCATG", IUPAC.ambiguous_dna)
array_seq = MutableSeq(array.array("c", "TCAAAAGGATGCATCATG"),
IUPAC.ambiguous_dna)
converted_seq = s.tomutable()
for test_seq in [string_seq]:
print repr(test_seq)
print test_seq.tostring()
print len(test_seq)
print repr(test_seq.toseq())
print test_seq[0]
print repr(test_seq[1:5])
test_seq[1:3] = "GAT"
print "Set slice with string:", repr(test_seq)
test_seq[1:3] = test_seq[5:7]
print "Set slice with MutableSeq:", repr(test_seq)
test_seq[1:3] = array.array("c", "GAT")
print "Set slice with array:", repr(test_seq)
test_seq[3] = "G"
print "Set item:", repr(test_seq)
del test_seq[4:5]
print "Delete slice:", repr(test_seq)
del test_seq[3]
print "Delete item:", repr(test_seq)
test_seq.append("C")
print "Append:", repr(test_seq)
test_seq.insert(4, "G")
print "Insert:", repr(test_seq)
print "Pop off the last item:", test_seq.pop()
test_seq.remove("G")
print "Removed Gs:", repr(test_seq)
try:
test_seq.remove("Z")
raise AssertionError("Did not get expected value error.")
except ValueError:
print "Expected value error and got it"
print "A count:", test_seq.count("A")
print "A index:", test_seq.index("A")
test_seq.reverse()
print "Reversed Seq:", repr(test_seq)
print "Reverse using -1 stride:", repr(test_seq[::-1])
test_seq.extend("GAT")
test_seq.extend(MutableSeq("TTT", IUPAC.ambiguous_dna))
print "Extended Seq:", repr(test_seq)
del test_seq[4:6:-1]
print "Delete stride slice:", repr(test_seq)
print "Extract every third nucleotide (slicing with stride 3):"
print repr(test_seq[0::3])
print repr(test_seq[1::3])
print repr(test_seq[2::3])
print "Setting wobble codon to N (set slice with stride 3):"
test_seq[2::3] = "N" * len(test_seq[2::3])
print repr(test_seq)
###########################################################################
from Bio.Data.IUPACData import ambiguous_dna_complement, ambiguous_rna_complement
from Bio.Data.IUPACData import ambiguous_dna_values, ambiguous_rna_values
from sets import Set
print
print "Checking ambiguous complements"
print "=============================="
#See bug 2380, Bio.Nexus was polluting the dictionary.
assert "-" not in ambiguous_dna_values
assert "?" not in ambiguous_dna_values
def complement(sequence) :
#TODO - Add a complement function to Bio/Seq.py?
#There is already a complement method on the Seq and MutableSeq objects.
return Seq.reverse_complement(sequence)[::-1]
print
print "DNA Ambiguity mapping:", ambiguous_dna_values
print "DNA Complement mapping:", ambiguous_dna_complement
for ambig_char, values in ambiguous_dna_values.iteritems() :
compl_values = complement(values)
print "%s={%s} --> {%s}=%s" % \
(ambig_char, values, compl_values, ambiguous_dna_complement[ambig_char])
assert Set(compl_values) == Set(ambiguous_dna_values[ambiguous_dna_complement[ambig_char]])
print
print "RNA Ambiguity mapping:", ambiguous_rna_values
print "RNA Complement mapping:", ambiguous_rna_complement
for ambig_char, values in ambiguous_rna_values.iteritems() :
compl_values = complement(values).replace("T","U") #need to help as no alphabet
print "%s={%s} --> {%s}=%s" % \
(ambig_char, values, compl_values, ambiguous_rna_complement[ambig_char])
assert Set(compl_values) == Set(ambiguous_rna_values[ambiguous_rna_complement[ambig_char]])
print
print "Reverse complements:"
for sequence in [Seq.Seq("".join(ambiguous_rna_values)),
Seq.Seq("".join(ambiguous_dna_values)),
Seq.Seq("".join(ambiguous_rna_values), Alphabet.generic_rna),
Seq.Seq("".join(ambiguous_dna_values), Alphabet.generic_dna),
Seq.Seq("".join(ambiguous_rna_values), IUPAC.IUPACAmbiguousRNA()),
Seq.Seq("".join(ambiguous_dna_values), IUPAC.IUPACAmbiguousDNA()),
Seq.Seq("AWGAARCKG")]: # Note no U or T
print "%s -> %s" \
% (repr(sequence), repr(Seq.reverse_complement(sequence)))
assert sequence.tostring() \
== Seq.reverse_complement(Seq.reverse_complement(sequence)).tostring(), \
"Dobule reverse complement didn't preserve the sequence!"
print
###########################################################################
test_seqs = [s,t,u,
Seq.Seq("ATGAAACTG"),
#TODO - Fix ambiguous translation
#Seq.Seq("ATGAARCTG"),
#Seq.Seq("AWGAARCKG"), # Note no U or T
#Seq.Seq("".join(ambiguous_rna_values)),
#Seq.Seq("".join(ambiguous_dna_values)),
#Seq.Seq("".join(ambiguous_rna_values), Alphabet.generic_rna),
#Seq.Seq("".join(ambiguous_dna_values), Alphabet.generic_dna),
#Seq.Seq("".join(ambiguous_rna_values), IUPAC.IUPACAmbiguousDNA()),
#Seq.Seq("".join(ambiguous_dna_values), IUPAC.IUPACAmbiguousRNA()),
#Seq.Seq("AWGAARCKG", Alphabet.generic_dna),
Seq.Seq("AUGAAACUG", Alphabet.generic_dna),
Seq.Seq("ATGAAACTG", Alphabet.generic_rna),
Seq.Seq("ATGAAACTG", Alphabet.generic_nucleotide),
Seq.Seq("AUGAAACTG", Alphabet.generic_nucleotide), #U and T
Seq.MutableSeq("ATGAAACTG", Alphabet.generic_rna),
Seq.Seq("ACTGTCGTCT", Alphabet.generic_protein)]
print
print "Transcribe DNA into RNA"
print "======================="
for nucleotide_seq in test_seqs:
try :
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(Seq.transcribe(nucleotide_seq)))
except ValueError, e :
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
print
print "Back-transcribe RNA into DNA"
print "============================"
for nucleotide_seq in test_seqs:
try :
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(Seq.transcribe(nucleotide_seq)))
except ValueError, e :
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
print
print "Reverse Complement"
print "=================="
for nucleotide_seq in test_seqs:
try :
print "%s\n-> %s" \
% (repr(nucleotide_seq) , repr(Seq.reverse_complement(nucleotide_seq)))
except ValueError, e :
print "%s\n-> %s" \
% (repr(nucleotide_seq) , str(e))
print
print "Translating"
print "==========="
for nucleotide_seq in test_seqs:
try :
print "%s\n-> %s" \
% (repr(nucleotide_seq) , repr(Seq.translate(nucleotide_seq)))
except ValueError, e :
print "%s\n-> %s" \
% (repr(nucleotide_seq) , str(e))
print
print "Seq's .complement() method"
print "=========================="
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq, Seq.Seq) :
try :
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(nucleotide_seq.complement()))
assert nucleotide_seq.complement().tostring() \
== Seq.reverse_complement(nucleotide_seq).tostring()[::-1], \
"Bio.Seq function and method disagree!"
except ValueError, e :
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
print
print "Seq's .reverse_complement() method"
print "=================================="
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq, Seq.Seq) :
try :
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(nucleotide_seq.reverse_complement()))
assert nucleotide_seq.reverse_complement().tostring() \
== Seq.reverse_complement(nucleotide_seq).tostring(), \
"Bio.Seq function and method disagree!"
except ValueError, e :
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
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