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Represents a classical multiple sequence alignment (MSA).

By this we mean a collection of sequences (usually shown as rows) which
are all the same length (usually with gap characters for insertions or
padding). The data can then be regarded as a matrix of letters, with well
defined columns.

You would typically create an MSA by loading an alignment file with the
AlignIO module:
(more...)

src/b/i/biopython-HEAD/Bio/FSSP/FSSPTools.py   biopython(Download)
from Bio import FSSP
import copy
from Bio.Align import MultipleSeqAlignment
from Bio import Alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
 
class FSSPAlign(MultipleSeqAlignment):
            mult_align_dict[j] += align_dict.abs(i).pos_align_dict[j].aa
    alpha = Alphabet.Gapped(Alphabet.IUPAC.extended_protein)
    fssp_align = MultipleSeqAlignment([], alphabet=alpha)
    for i in sorted(mult_align_dict):
        fssp_align.append(SeqRecord(Seq(mult_align_dict[i], alpha),

src/b/i/bioscripts.convert-0.4/bioscripts/convert/convbioseq.py   bioscripts.convert(Download)
		if out_fmt in ['nexus']:
			# need to hack to handle this crap
			from Bio.Align import MultipleSeqAlignment
			aln = MultipleSeqAlignment(in_seqs,
				alphabet=opts.seqtype or BIOSEQ_ALPHABET_PROTEIN)

src/b/i/biofrills-0.3.1/biofrills/alnutils.py   biofrills(Download)
 
from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
        newrec.seq = seq
        clean_recs.append(newrec)
    return MultipleSeqAlignment(clean_recs, alphabet=alphabet)
 
 

src/b/i/biopython-HEAD/Bio/SearchIO/_model/hsp.py   biopython(Download)
 
from Bio import BiopythonWarning
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
    def _aln_get(self):
        if self.query is None and self.hit is None:
            return None
        elif self.hit is None:
            return MultipleSeqAlignment([self.query], self.alphabet)
        elif self.query is None:
            return MultipleSeqAlignment([self.hit], self.alphabet)
        else:
            return MultipleSeqAlignment([self.query, self.hit], self.alphabet)

src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlignment.py   biopython(Download)
__docformat__ = "epytext en"  # Don't just use plain text in epydoc API pages!
 
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
 
from Bio.CodonAlign.CodonAlphabet import default_codon_table, default_codon_alphabet
from Bio.CodonAlign.CodonSeq import _get_codon_list, CodonSeq, cal_dn_ds
from Bio.CodonAlign.chisq import chisqprob
 
class CodonAlignment(MultipleSeqAlignment):
            if alphabet is None:
                from Bio.Alphabet import generic_nucleotide
                return MultipleSeqAlignment((rec[col_index] for rec in \
                                                    self._records[row_index]),
                                             generic_nucleotide)
            else:
                return MultipleSeqAlignment((rec[col_index] for rec in \
        alignments = [SeqRecord(rec.seq.toSeq(), id=rec.id) for \
                rec in self._records]
        return MultipleSeqAlignment(alignments)
 
    def get_dn_ds_matrix(self, method="NG86"):

src/b/i/biopython-1.63/Bio/SearchIO/_model/hsp.py   biopython(Download)
 
from Bio import BiopythonWarning
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
    def _aln_get(self):
        if self.query is None and self.hit is None:
            return None
        elif self.hit is None:
            return MultipleSeqAlignment([self.query], self.alphabet)
        elif self.query is None:
            return MultipleSeqAlignment([self.hit], self.alphabet)
        else:
            return MultipleSeqAlignment([self.query, self.hit], self.alphabet)

src/b/i/biopython-HEAD/Bio/Phylo/PhyloXML.py   biopython(Download)
 
from Bio import Alphabet
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqFeature import SeqFeature, FeatureLocation
        except StopIteration:
            # No aligned sequences were found --> empty MSA
            return MultipleSeqAlignment([])
        msa = MultipleSeqAlignment([first_seq.to_seqrecord()],
                                   first_seq.get_alphabet())

src/b/i/biopython-HEAD/Bio/AlignIO/__init__.py   biopython(Download)
#   http://www.bioperl.org/wiki/MSF_multiple_alignment_format
 
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
            records.append(record)
            if len(records) == seq_count:
                yield MultipleSeqAlignment(records, alphabet)
                records = []
        if len(records) > 0:
        records = list(SeqIO.parse(handle, format, alphabet))
        if records:
            yield MultipleSeqAlignment(records, alphabet)
    raise StopIteration
 

src/b/i/biopython-1.63/Bio/Phylo/PhyloXML.py   biopython(Download)
 
from Bio import Alphabet
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqFeature import SeqFeature, FeatureLocation
        except StopIteration:
            # No aligned sequences were found --> empty MSA
            return MultipleSeqAlignment([])
        msa = MultipleSeqAlignment([first_seq.to_seqrecord()],
                                   first_seq.get_alphabet())

src/b/i/biopython-1.63/Bio/AlignIO/__init__.py   biopython(Download)
#   http://www.bioperl.org/wiki/MSF_multiple_alignment_format
 
from Bio.Align import MultipleSeqAlignment
from Bio.Align.Generic import Alignment
from Bio.Alphabet import Alphabet, AlphabetEncoder, _get_base_alphabet
            records.append(record)
            if len(records) == seq_count:
                yield MultipleSeqAlignment(records, alphabet)
                records = []
        if len(records) > 0:
        records = list(SeqIO.parse(handle, format, alphabet))
        if records:
            yield MultipleSeqAlignment(records, alphabet)
    raise StopIteration
 

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