def test_back_transcription_of_proteins(self):
"""Test back-transcription shouldn't work on a protein!"""
for s in protein_seqs:
with self.assertRaises(ValueError):
Seq.back_transcribe(s)
if isinstance(s, Seq.Seq):
with self.assertRaises(ValueError):
s.back_transcribe()
def test_back_transcription_of_proteins(self):
"""Test back-transcription shouldn't work on a protein!"""
for s in protein_seqs:
with self.assertRaises(ValueError):
Seq.back_transcribe(s)
if isinstance(s, Seq.Seq):
with self.assertRaises(ValueError):
s.back_transcribe()
def test_back_transcribe_rna_into_dna(self):
for nucleotide_seq in test_seqs:
expected = Seq.back_transcribe(nucleotide_seq)
self.assertEqual(
str(nucleotide_seq).replace("u", "t").replace("U", "T"),
str(expected),
)
def test_seq_object_back_transcription_method(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet) and \
isinstance(nucleotide_seq, Seq.Seq):
expected = Seq.back_transcribe(nucleotide_seq)
self.assertEqual(repr(nucleotide_seq.back_transcribe()),
repr(expected))
def test_back_transcribe_rna_into_dna(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet):
expected = Seq.back_transcribe(nucleotide_seq)
self.assertEqual(
str(nucleotide_seq).replace("u", "t").replace("U", "T"),
str(expected))
def reversed_transcription(self):
"""Given the seq of type RNA transcribes it to DNA.
:return: Seq object of type DNA.
"""
if self.s_type != 'RNA':
raise TypeError(
'Sequence type {} can not be transcribed in reverse.'.format(
self.s_type))
return Seq.back_transcribe(self.seq)
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_back_transcribe_rna_string_into_dna(self):
seq = "AUGAAACUG"
self.assertEqual("ATGAAACTG", Seq.back_transcribe(seq))
except ValueError:
pass
if not isinstance(s, Seq.Seq):
continue # Only Seq has this method
try:
print s.transcribe()
assert False, "Transcription shouldn't work on a protein!"
except ValueError:
pass
print
print "Back-transcribe RNA into DNA"
print "============================"
for nucleotide_seq in test_seqs:
try:
expected = Seq.back_transcribe(nucleotide_seq)
assert str(nucleotide_seq).replace("u",
"t").replace("U",
"T") == 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.back_transcribe())
except ValueError:
assert expected is None
assert False, "Transcription shouldn't work on a protein!"
except ValueError :
pass
if not isinstance(s, Seq.Seq) : continue #Only Seq has this method
try :
print s.transcribe()
assert False, "Transcription shouldn't work on a protein!"
except ValueError :
pass
print
print "Back-transcribe RNA into DNA"
print "============================"
for nucleotide_seq in test_seqs:
try :
expected = Seq.back_transcribe(nucleotide_seq)
assert str(nucleotide_seq).replace("u","t").replace("U","T") == 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.back_transcribe())
except ValueError :
assert expected is None
for s in protein_seqs :
# -*- coding: utf-8 -*-
"""
Created on Fri Jun 21 12:38:35 2019
@author: kaysm
"""
from Bio import Seq
Input = open("Translate an RNA String into an Amino Acid String.txt", "r")
sequence = Input.read().split("\n")[0]
Dna = Seq.back_transcribe(sequence)
print(Seq.translate(Dna))
def test_seq_object_back_transcription_method(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet) and \
isinstance(nucleotide_seq, Seq.Seq):
expected = Seq.back_transcribe(nucleotide_seq)
self.assertEqual(repr(nucleotide_seq.back_transcribe()), repr(expected))
def test_back_transcribe_rna_string_into_dna(self):
seq = "AUGAAACUG"
self.assertEqual("ATGAAACTG", Seq.back_transcribe(seq))
def test_back_transcribe_rna_into_dna(self):
for nucleotide_seq in test_seqs:
if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet):
expected = Seq.back_transcribe(nucleotide_seq)
self.assertEqual(str(nucleotide_seq).replace("u", "t").replace("U", "T"),
str(expected))
#print (record.description)
all_id = record.description
piRNA_product = all_id.split('|')[0]
piRNA_ID = ()
gb_search = re.search(".*\|gb\|.*", all_id)
if gb_search:
piRNA_ID = all_id.split('|')[2]
else:
piRNA_ID = "NULL"
#print (record.seq)
## transcribe back
dna_seq = Seq.back_transcribe(record.seq)
head = ">" + all_id + "\n"
output_FASTA.write(head)
output_FASTA.write(str(dna_seq))
output_FASTA.write("\n")
## parse and generate
Chr = all_id.split(':')[1]
Start = all_id.split(':')[2]
End = all_id.split(':')[3]
Strand = all_id.split(':')[-1]
## GTF example
code_strand = ()
if (Strand == 'Plus'):
