def UniprotIterator(handle, alphabet=Alphabet.ProteinAlphabet(), return_raw_comments=False):
"""Generator function to parse UniProt XML as SeqRecord objects.
parses an XML entry at a time from any UniProt XML file
returns a SeqRecord for each iteration
This generator can be used in Bio.SeqIO
return_raw_comments = True --> comment fields are returned as complete XML to allow further processing
skip_parsing_errors = True --> if parsing errors are found, skip to next entry
"""
if isinstance(alphabet, Alphabet.NucleotideAlphabet):
raise ValueError("Wrong alphabet %r" % alphabet)
if isinstance(alphabet, Alphabet.Gapped):
if isinstance(alphabet.alphabet, Alphabet.NucleotideAlphabet):
raise ValueError("Wrong alphabet %r" % alphabet)
if not hasattr(handle, "read"):
if isinstance(handle, str):
handle = StringIO(handle)
else:
raise Exception('An XML-containing handler or an XML string must be passed')
if ElementTree is None:
from SAP.Bio import MissingExternalDependencyError
raise MissingExternalDependencyError(
"No ElementTree module was found. "
"Use Python 2.5+, lxml or elementtree if you "
"want to use Bio.SeqIO.UniprotIO.")
for event, elem in ElementTree.iterparse(handle, events=("start", "end")):
if event == "end" and elem.tag == NS + "entry":
yield Parser(elem, alphabet=alphabet, return_raw_comments=return_raw_comments).parse()
elem.clear()
def molecular_weight(seq, seq_type=None, double_stranded=False, circular=False,
monoisotopic=False):
"""Calculates the molecular weight of a DNA, RNA or protein sequence.
Only unambiguous letters are allowed. Nucleotide sequences are assumed to
have a 5' phosphate.
seq: String or Biopython sequence object.
seq_type: The default (None) is to take the alphabet from the seq argument,
or assume DNA if the seq argument is a string. Override this with
a string 'DNA', 'RNA', or 'protein'.
double_stranded: Calculate the mass for the double stranded molecule?
circular: Is the molecule circular (has no ends)?
monoisotopic: Use the monoisotopic mass tables?
Note that for backwards compatibility, if the seq argument is a string,
or Seq object with a generic alphabet, and no seq_type is specified
(i.e. left as None), then DNA is assumed.
>>> print("%0.2f" % molecular_weight("AGC"))
949.61
>>> print("%0.2f" % molecular_weight(Seq("AGC")))
949.61
However, it is better to be explicit - for example with strings:
>>> print("%0.2f" % molecular_weight("AGC", "DNA"))
949.61
>>> print("%0.2f" % molecular_weight("AGC", "RNA"))
997.61
>>> print("%0.2f" % molecular_weight("AGC", "protein"))
249.29
Or, with the sequence alphabet:
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.Alphabet import generic_dna, generic_rna, generic_protein
>>> print("%0.2f" % molecular_weight(Seq("AGC", generic_dna)))
949.61
>>> print("%0.2f" % molecular_weight(Seq("AGC", generic_rna)))
997.61
>>> print("%0.2f" % molecular_weight(Seq("AGC", generic_protein)))
249.29
Also note that contradictory sequence alphabets and seq_type will also
give an exception:
>>> from SAP.Bio.Seq import Seq
>>> from SAP.Bio.Alphabet import generic_dna
>>> print("%0.2f" % molecular_weight(Seq("AGC", generic_dna), "RNA"))
Traceback (most recent call last):
...
ValueError: seq_type='RNA' contradicts DNA from seq alphabet
"""
# Rewritten by Markus Piotrowski, 2014
# Find the alphabet type
tmp_type = ''
if isinstance(seq, Seq) or isinstance(seq, MutableSeq):
base_alphabet = Alphabet._get_base_alphabet(seq.alphabet)
if isinstance(base_alphabet, Alphabet.DNAAlphabet):
tmp_type = 'DNA'
elif isinstance(base_alphabet, Alphabet.RNAAlphabet):
tmp_type = 'RNA'
elif isinstance(base_alphabet, Alphabet.ProteinAlphabet):
tmp_type = 'protein'
elif isinstance(base_alphabet, Alphabet.ThreeLetterProtein):
tmp_type = 'protein'
# Convert to one-letter sequence. Have to use a string for seq1
seq = Seq(seq1(str(seq)), alphabet=Alphabet.ProteinAlphabet())
elif not isinstance(base_alphabet, Alphabet.Alphabet):
raise TypeError("%s is not a valid alphabet for mass calculations"
% base_alphabet)
else:
tmp_type = "DNA" # backward compatibity
if seq_type and tmp_type and tmp_type != seq_type:
raise ValueError("seq_type=%r contradicts %s from seq alphabet"
% (seq_type, tmp_type))
seq_type = tmp_type
elif isinstance(seq, str):
if seq_type is None:
seq_type = "DNA" # backward compatibity
else:
raise TypeError("Expected a string or Seq object, not seq=%r" % seq)
seq = ''.join(str(seq).split()).upper() # Do the minimum formatting
if seq_type == 'DNA':
if monoisotopic:
weight_table = IUPACData.monoisotopic_unambiguous_dna_weights
else:
weight_table = IUPACData.unambiguous_dna_weights
elif seq_type == 'RNA':
if monoisotopic:
weight_table = IUPACData.monoisotopic_unambiguous_rna_weights
else:
weight_table = IUPACData.unambiguous_rna_weights
elif seq_type == 'protein':
if monoisotopic:
weight_table = IUPACData.monoisotopic_protein_weights
else:
weight_table = IUPACData.protein_weights
else:
raise ValueError("Allowed seq_types are DNA, RNA or protein, not %r"
% seq_type)
if monoisotopic:
water = 18.010565
else:
water = 18.0153
try:
weight = sum(weight_table[x] for x in seq) - (len(seq)-1) * water
if circular:
weight -= water
except KeyError as e:
raise ValueError('%s is not a valid unambiguous letter for %s'
%(e, seq_type))
except:
raise
if seq_type in ('DNA', 'RNA') and double_stranded:
seq = str(Seq(seq).complement())
weight += sum(weight_table[x] for x in seq) - (len(seq)-1) * water
if circular:
weight -= water
elif seq_type == 'protein' and double_stranded:
raise ValueError('double-stranded proteins await their discovery')
return weight
def __init__(self, elem, alphabet=Alphabet.ProteinAlphabet(), return_raw_comments=False):
self.entry = elem
self.alphabet = alphabet
self.return_raw_comments = return_raw_comments