def translate_seqs(seq_iter, gap_characters=['-'], **kwargs):
'''
Translates DNA or RNA sequences into amino acid sequences.
This function returns a generator that yields a copy of each input sequence
translated into an amino acid sequence (all `gap_characters` are removed
from the sequence prior to translation). `kwargs` are keyword arguments
that are passed to the Seq.translate method of biopython to translate each
sequence. Below is biopython's description of valid keyword arguments:
- table - Which codon table to use? This can be either a name
(string), an NCBI identifier (integer), or a CodonTable
object (useful for non-standard genetic codes). This
defaults to the "Standard" table.
- stop_symbol - Single character string, what to use for terminators.
This defaults to the asterisk, "*".
- to_stop - Boolean, defaults to False meaning do a full translation
continuing on past any stop codons (translated as the
specified stop_symbol). If True, translation is
terminated at the first in frame stop codon (and the
stop_symbol is not appended to the returned protein
sequence).
- cds - Boolean, indicates this is a complete CDS. If True,
this checks the sequence starts with a valid alternative start
codon (which will be translated as methionine, M), that the
sequence length is a multiple of three, and that there is a
single in frame stop codon at the end (this will be excluded
from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised.
'''
for s in remove_gaps(seq_iter, gap_characters=gap_characters):
yield sequtils.get_translation(seq_record=s, **kwargs)
def translate_seqs(seq_iter,
gap_characters=['-'],
**kwargs):
'''
Translates DNA or RNA sequences into amino acid sequences.
This function returns a generator that yields a copy of each input sequence
translated into an amino acid sequence (all `gap_characters` are removed
from the sequence prior to translation). `kwargs` are keyword arguments
that are passed to the Seq.translate method of biopython to translate each
sequence. Below is biopython's description of valid keyword arguments:
- table - Which codon table to use? This can be either a name
(string), an NCBI identifier (integer), or a CodonTable
object (useful for non-standard genetic codes). This
defaults to the "Standard" table.
- stop_symbol - Single character string, what to use for terminators.
This defaults to the asterisk, "*".
- to_stop - Boolean, defaults to False meaning do a full translation
continuing on past any stop codons (translated as the
specified stop_symbol). If True, translation is
terminated at the first in frame stop codon (and the
stop_symbol is not appended to the returned protein
sequence).
- cds - Boolean, indicates this is a complete CDS. If True,
this checks the sequence starts with a valid alternative start
codon (which will be translated as methionine, M), that the
sequence length is a multiple of three, and that there is a
single in frame stop codon at the end (this will be excluded
from the protein sequence, regardless of the to_stop option).
If these tests fail, an exception is raised.
'''
for s in remove_gaps(seq_iter, gap_characters=gap_characters):
yield sequtils.get_translation(seq_record = s, **kwargs)
def test_extra_base(self):
s1 = SeqRecord(Seq('ATGACCAACTGAATAA', IUPAC.unambiguous_dna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertFalse(s1 is s2)
self.assertEqual(str(s2.seq), 'MTN*I')
def test_to_stop(self):
s1 = SeqRecord(Seq('ATGACCAACTGA', IUPAC.unambiguous_dna), id='1')
s2 = sequtils.get_translation(s1, to_stop=True)
self.assertSameMetadata(s1, s2)
self.assertFalse(s1 is s2)
self.assertEqual(str(s2.seq), 'MTN')
def test_ambiguous_rna(self):
s1 = SeqRecord(Seq('AUGAURAACUGA', IUPAC.ambiguous_rna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertFalse(s1 is s2)
self.assertEqual(str(s2.seq), 'MXN*')
def test_extra_base(self):
s1 = SeqRecord(Seq('ATGACCAACTGAATAA', IUPAC.unambiguous_dna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertNotEqual(s1, s2)
self.assertEqual(str(s2.seq), 'MTN*I')
def test_to_stop(self):
s1 = SeqRecord(Seq('ATGACCAACTGA', IUPAC.unambiguous_dna), id='1')
s2 = sequtils.get_translation(s1, to_stop = True)
self.assertSameMetadata(s1, s2)
self.assertNotEqual(s1, s2)
self.assertEqual(str(s2.seq), 'MTN')
def test_ambiguous_rna(self):
s1 = SeqRecord(Seq('AUGAURAACUGA', IUPAC.ambiguous_rna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertNotEqual(s1, s2)
self.assertEqual(str(s2.seq), 'MXN*')
def test_ambiguous_dna(self):
s1 = SeqRecord(Seq('ATGATRAACTGA', IUPAC.ambiguous_dna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertFalse(s1 is s2)
self.assertEqual(str(s2.seq), 'MXN*')
def test_unambiguous_rna(self):
s1 = SeqRecord(Seq('AUGACCAACUGA', IUPAC.unambiguous_rna), id='1')
s2 = sequtils.get_translation(s1)
self.assertSameMetadata(s1, s2)
self.assertFalse(s1 is s2)
self.assertEqual(str(s2.seq), 'MTN*')
