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A SeqRecord object holds a sequence and information about it.

Main attributes:
 - id          - Identifier such as a locus tag (string)
 - seq         - The sequence itself (Seq object or similar)

Additional attributes:
 - name        - Sequence name, e.g. gene name (string)
 - description - Additional text (string)
 - dbxrefs     - List of database cross references (list of strings)(more...)

src/p/y/pytools-HEAD/seqtools.py   pytools(Download)
from Bio            import Alphabet
from Bio.Seq        import Seq
from Bio.SeqRecord  import SeqRecord
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio            import pairwise2
def make_SeqRecord(name,seq):
    return SeqRecord(Seq(seq),id=name,name=name,description=name)
 
 
def get_string(seqobj):
def complicateSeqRecord(obj):
    if '__SeqRecord__' not in obj:
        raise ValueError, "object must be converable to Bio.SeqRecord"
    features = map(complicateSeqFeature,obj['features'])
    record = SeqRecord(seq=complicateSeq(obj['seq']),id=obj['id'],name=obj['name'],description=obj['description'],dbxrefs=obj['dbxrefs'],features=features,annotations=obj['annotations'],letter_annotations=obj['letter_annotations'])

src/b/i/biofrills-0.3.1/biofrills/alnutils.py   biofrills(Download)
from Bio.Align import MultipleSeqAlignment
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
 
                  for row in zip(*clean_cols)]
    for rec, clean_seq in zip(records, clean_seqs):
        yield SeqRecord(Seq(clean_seq, rec.seq.alphabet), id=rec.id,
                        name=rec.name, description=rec.description,
                        dbxrefs=rec.dbxrefs, features=rec.features,

src/b/i/biopython-HEAD/Bio/SeqIO/AbiIO.py   biopython(Download)
from Bio.Alphabet.IUPAC import ambiguous_dna, unambiguous_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
from Bio._py3k import _bytes_to_string, _as_bytes
        file_name = ""
 
    record = SeqRecord(Seq(seq, alphabet),
                       id=sample_id, name=file_name,
                       description='',

src/b/i/biopython-1.63/Bio/SeqIO/AbiIO.py   biopython(Download)
from Bio.Alphabet.IUPAC import ambiguous_dna, unambiguous_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
from Bio._py3k import _bytes_to_string, _as_bytes
        file_name = ""
 
    record = SeqRecord(Seq(seq, alphabet),
                       id=sample_id, name=file_name,
                       description='',

src/p/y/PySang-0.3.2/pysang/parser.py   PySang(Download)
from Bio.Alphabet.IUPAC import ambiguous_dna, unambiguous_dna
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio._py3k import _bytes_to_string, _as_bytes
 
        file_name = ""
 
    record = SeqRecord(Seq(seq, alphabet),
                       id=sample_id, name=file_name,
                       description='',

src/c/l/clusterDbAnalysis-HEAD/scripts/kbaseGenomeToGenbank.py   clusterDbAnalysis(Download)
from Bio.Alphabet import IUPAC
from Bio.SeqFeature import SeqFeature, FeatureLocation
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
 
    for contig in contig_to_feature_data:
        seq = Seq(contig_to_sequence[contig], IUPAC.ambiguous_dna)
        record = SeqRecord(seq, id=sanitizeString(contig, False), description = "%s contig %s" %(organism_name, contig), name=contig, features=contig_to_feature_data[contig], annotations=annotations)
        records.append(record)
    SeqIO.write(records, sys.stdout, "genbank")

src/b/i/biopython-HEAD/Bio/AlignIO/FastaIO.py   biopython(Download)
 
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import single_letter_alphabet, generic_dna, generic_protein
        #Query
        #=====
        record = SeqRecord(Seq(q, alphabet),
                           id=query_id,
                           name="query",
        #Match
        #=====
        record = SeqRecord(Seq(m, alphabet),
                           id=match_id,
                           name="match",

src/b/i/biopython-1.63/Bio/AlignIO/FastaIO.py   biopython(Download)
 
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Align import MultipleSeqAlignment
from Bio.Alphabet import single_letter_alphabet, generic_dna, generic_protein
        #Query
        #=====
        record = SeqRecord(Seq(q, alphabet),
                           id=query_id,
                           name="query",
        #Match
        #=====
        record = SeqRecord(Seq(m, alphabet),
                           id=match_id,
                           name="match",

src/b/i/biopython-HEAD/Bio/SearchIO/_model/hsp.py   biopython(Download)
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
from Bio._utils import getattr_str, trim_str
            seq.seq.alphabet = self.alphabet
        elif isinstance(seq, basestring):
            seq = SeqRecord(Seq(seq, self.alphabet), id=seq_id, name=seq_name,
                    description=seq_desc, features=seq_feats)
 

src/b/i/biopython-1.63/Bio/SearchIO/_model/hsp.py   biopython(Download)
from Bio.Alphabet import single_letter_alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
 
from Bio._utils import getattr_str, trim_str
            seq.seq.alphabet = self.alphabet
        elif isinstance(seq, basestring):
            seq = SeqRecord(Seq(seq, self.alphabet), id=seq_id, name=seq_name,
                    description=seq_desc, features=seq_feats)
 

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