def test_transcription_of_proteins(self):
"""Test transcription shouldn't work on a protein!"""
for s in protein_seqs:
with self.assertRaises(ValueError):
Seq.transcribe(s)
if isinstance(s, Seq.Seq):
with self.assertRaises(ValueError):
s.transcribe()
def test_transcription_of_proteins(self):
"""Test transcription shouldn't work on a protein!"""
for s in protein_seqs:
with self.assertRaises(ValueError):
Seq.transcribe(s)
if isinstance(s, Seq.Seq):
with self.assertRaises(ValueError):
s.transcribe()
def test_seq_object_transcription_method(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq, Seq.Seq):
self.assertEqual(
repr(Seq.transcribe(nucleotide_seq)),
repr(nucleotide_seq.transcribe()),
)
def test_transcription_dna_into_rna(self):
for nucleotide_seq in test_seqs:
expected = Seq.transcribe(nucleotide_seq)
self.assertEqual(
str(nucleotide_seq).replace("t", "u").replace("T", "U"),
str(expected),
)
def test_transcription_dna_into_rna(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet):
expected = Seq.transcribe(nucleotide_seq)
self.assertEqual(
str(nucleotide_seq).replace("t", "u").replace("T", "U"),
str(expected))
def print_proteins_and_codons_using_mitocondrial_yeast_table(seq):
dna = Seq(seq)
mRna = dna.transcribe()
#Diccionario
d = {}
d["mRNA"] = [mRna]
d["protein"] = []
d["stop_codon"] = []
#Revisar si tiene codon de inicio
codon_inicio = False
for codon in range(0,len(dna),3):
if "ATG" in dna[codon:codon+3]:
#Variable con la posicion del primer aa del codon de inicio
posicion_inicio = codon
dnaCoding = dna[codon:len(dna)]
d["protein"] = dnaCoding.translate(to_stop = True, table = 3)
#Si hay codon de inicio
codon_inicio = True
#Solo para encontrar un codon
break
if "ATA" in dna[codon:codon+3]:
#Variable con la posicion del primer aa del codon de inicio
posicion_inicio = codon
dnaCoding = dna[codon:len(dna)]
d["protein"] = dnaCoding.translate(to_stop = True, table = 3)
#Si hay codon de inicio
codon_inicio = True
#Solo para encontrar un codon
break
if "GTG" in dna[codon:codon+3]:
#Variable con la posicion del primer aa del codon de inicio
posicion_inicio = codon
dnaCoding = dna[codon:len(dna)]
d["protein"] = dnaCoding.translate(to_stop = True, table = 3)
#Si hay codon de inicio
codon_inicio = True
#Solo para encontrar un codon
break
#Si si lo hay buscar codon de paro despues del codon de inicio
if codon_inicio == True:
for codon in range(0,len(dna),3):
#print(dna[codon:codon+3])
if ("TAG" in dna[codon:codon+3]) & (posicion_inicio < codon):
d["stop_codon"].append("TAG")
break
if ("TAA" in dna[codon:codon+3]) & (posicion_inicio < codon):
d["stop_codon"].append("TAA")
break
return d
def dna_aa():
if session.username == None:
redirect(URL(r=request, c='account', f='log_in'))
form = FORM(
TABLE(
TR(
'Sequence (raw format): ',
TEXTAREA(_type='text',
_name='sequence',
requires=IS_NOT_EMPTY())),
#TR("Sequence Type: ",
# SELECT("Raw Format", "FASTA",
# _name="seq_type")),
TR(
'Action: ',
SELECT('Complementation',
'Transcribe',
'Translate',
'Back Transcribe',
'Back Translate',
_name='action'), INPUT(_type='submit',
_value='SUBMIT'))))
if form.accepts(request.vars, session):
#if form.vars.seq_type == "FASTA":
# session['sequence'] = \
# seqClean(fasta_to_raw(form.vars.sequence.upper()))
#else:
session['sequence'] = seqClean(form.vars.sequence.upper())
if form.vars.action == "Complementation":
session['action'] = "Complementation"
session['Complement'] = Seq.reverse_complement(session['sequence'])
if form.vars.action == "Transcribe":
session['action'] = 'Transcribe'
session['Transcribed RNA'] = Seq.transcribe(session['sequence'])
if form.vars.action == "Back Transcribe":
session['action'] = 'Back Transcribe'
session['DNA'] = Seq.back_transcribe(session['sequence'])
if form.vars.action == "Translate":
session['action'] = 'Translate'
session.update(translate(session['sequence']))
if form.vars.action == "Back Translate":
session['action'] = 'Back Translate'
session.update(back_translate(session['sequence']))
redirect(URL(r=request, f='dna_aa_output'))
return dict(form=form)
def dna_aa():
if session.username == None:
redirect(URL(r=request, c='account', f='log_in'))
form = FORM(TABLE(TR('Sequence (raw format): ',
TEXTAREA(_type='text', _name='sequence',
requires=IS_NOT_EMPTY())),
#TR("Sequence Type: ",
# SELECT("Raw Format", "FASTA",
# _name="seq_type")),
TR('Action: ',
SELECT('Complementation', 'Transcribe', 'Translate',
'Back Transcribe', 'Back Translate',
_name='action'),
INPUT(_type='submit', _value='SUBMIT'))))
if form.accepts(request.vars,session):
#if form.vars.seq_type == "FASTA":
# session['sequence'] = \
# seqClean(fasta_to_raw(form.vars.sequence.upper()))
#else:
session['sequence'] = seqClean(form.vars.sequence.upper())
if form.vars.action == "Complementation":
session['action'] = "Complementation"
session['Complement'] = Seq.reverse_complement(session['sequence'])
if form.vars.action == "Transcribe":
session['action'] = 'Transcribe'
session['Transcribed RNA'] = Seq.transcribe(session['sequence'])
if form.vars.action == "Back Transcribe":
session['action'] = 'Back Transcribe'
session['DNA'] = Seq.back_transcribe(session['sequence'])
if form.vars.action == "Translate":
session['action'] = 'Translate'
session.update(translate(session['sequence']))
if form.vars.action == "Back Translate":
session['action'] = 'Back Translate'
session.update(back_translate(session['sequence']))
redirect(URL(r=request, f='dna_aa_output'))
return dict(form=form)
def test_transcription_dna_string_into_rna(self):
seq = "ATGAAACTG"
self.assertEqual("AUGAAACUG", Seq.transcribe(seq))
#Sanity test on the test sequence alphabets (see also enhancement bug 2597)
for nucleotide_seq in test_seqs:
if hasattr(nucleotide_seq, "alphabet"):
if "U" in str(nucleotide_seq).upper():
assert not isinstance(nucleotide_seq.alphabet,
Alphabet.DNAAlphabet)
if "T" in str(nucleotide_seq).upper():
assert not isinstance(nucleotide_seq.alphabet,
Alphabet.RNAAlphabet)
print
print "Transcribe DNA into RNA"
print "======================="
for nucleotide_seq in test_seqs:
try:
expected = Seq.transcribe(nucleotide_seq)
assert str(nucleotide_seq).replace("t",
"u").replace("T",
"U") == str(expected)
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(expected))
except ValueError, e:
expected = None
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
#Now test the Seq object's method
if isinstance(nucleotide_seq, Seq.Seq):
try:
assert repr(expected) == repr(nucleotide_seq.transcribe())
except ValueError:
assert expected is None
# Import the sequence from the Biopython library
from Bio.Seq import *
def complement(seq):
comp_seq=""
mapping = {'A':'T', "C":"G", "G":"C", "T":"A"}
for nucleotide in gene:
comp_seq += mapping[nucleotide]
return comp_seq;
def reverse(seq):
rev_seq = seq[::-1]
return rev_seq
if __name__ == '__main__':
gene = "TCAGACTGGTGCCGTGGTGCTCTCGCCCGATGTGACGTCGACCGCCAGCGGCGCGATGACGCCGAGGATTTCCGTGATCGTTTCGGAGGGCACGCCGGCTGCGGTCAGCGCGTCGGCCAAGTGTCCGGCGACCAGGCTGAAGTGGTGCATGGTAATTCCGCGCCCCTGATGGACTTGCTTCATCGGCGCACCGGTATAGGGCTCGGGCCCGCCAAGCGCGGCCGCGAAAAACTCCACCTGCTTGCCCTTGAGGCGGCTCATGTTCGTACCGCTGAAGAAGGCCGATAGTTGGTCATCGGCAAGCACACGAACATAGAAGTCCTCGACGACGACTTCGATGGCCTCATGCCCGCCGATCTTGTCGTAGATGCTGATCGGCTCACGTTTGCGCAAGCGTGACAGTAGTCCCATTTTTATA"
res = reverse(complement(gene))
print(res)
# Define a sequence as a DNA Seq object
seq = Seq("CCTCAGCGAGGACAGCAAGGGACTAGCC")
# The complement() method can act just like your complement() function.
complement = seq.complement()
# Similarly, we can use the reverse_complement() method.
reverse_complement = seq.reverse_complement()
# We can even use the transcribe() method to switch alphabets to RNA
RNA = seq.transcribe()
print(RNA)
#Sanity test on the test sequence alphabets (see also enhancement bug 2597)
for nucleotide_seq in test_seqs :
if hasattr(nucleotide_seq, "alphabet") :
if "U" in str(nucleotide_seq).upper() :
assert not isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet)
if "T" in str(nucleotide_seq).upper() :
assert not isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet)
print
print "Transcribe DNA into RNA"
print "======================="
for nucleotide_seq in test_seqs:
try :
expected = Seq.transcribe(nucleotide_seq)
assert str(nucleotide_seq).replace("t","u").replace("T","U") == str(expected)
print "%s -> %s" \
% (repr(nucleotide_seq) , repr(expected))
except ValueError, e :
expected = None
print "%s -> %s" \
% (repr(nucleotide_seq) , str(e))
#Now test the Seq object's method
if isinstance(nucleotide_seq, Seq.Seq) :
try :
assert repr(expected) == repr(nucleotide_seq.transcribe())
except ValueError :
assert expected is None
for s in protein_seqs :
print("Stop found:", seqs[temp_window:temp_window + 3])
temp_result.append(
temp_window +
3) # Stores stop codon index in list with start codon.
break
temp_window += 3 # Iterates by 3, codon size.
# print(temp_result)
# print(seqs[temp_result[0]: temp_result[1]])
# result_seqs.append(seqs[temp_result[0]: temp_result[1]])
# Adds protein to list from stored index locations, only if a stop codon is present at the end e.g.
# a stop codon was found before the end of the sequence.
try:
dna = seqs[temp_result[0]:temp_result[1]]
rna = Seq.transcribe(dna)
protein = Seq.translate(rna, stop_symbol="")
print(protein)
if protein not in result_seqs: # Stops the addition of duplicate peptides
result_seqs.append(protein)
except IndexError:
pass
window += 1
print(result_seqs)
# Writes sequences to file.
file = open("result_peptides.txt", "w")
def transcription(seqData):
dnaSeq = Seq(seqData[::-1])
return dnaSeq.transcribe()
#manipulateSeqFromFile("data/dna_chromosome_1.seq")
def test_seq_object_transcription_method(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet) and \
isinstance(nucleotide_seq, Seq.Seq):
self.assertEqual(repr(Seq.transcribe(nucleotide_seq)),
repr(nucleotide_seq.transcribe()))
def test_transcription_dna_string_into_rna(self):
seq = "ATGAAACTG"
self.assertEqual("AUGAAACUG", Seq.transcribe(seq))
def test_transcription_dna_into_rna(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet):
expected = Seq.transcribe(nucleotide_seq)
self.assertEqual(str(nucleotide_seq).replace("t", "u").replace("T", "U"),
str(expected))
