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src/b/i/biopython-1.63/Doc/examples/make_subsmat.py   biopython(Download)
from Bio import SubsMat
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import AlignInfo
 
# get an alignment object from a Clustalw alignment output
c_align = AlignIO.read('protein.aln', 'clustal',
                       alphabet=Gapped(IUPAC.protein))

src/b/i/biopython-1.63/Doc/examples/clustal_run.py   biopython(Download)
 
# biopython
from Bio.Alphabet import Gapped, IUPAC
from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO
# Parse the output
alignment = AlignIO.read("test.aln", "clustal",
                         alphabet=Gapped(IUPAC.unambiguous_dna))
 
print(alignment)

src/b/i/biopython-HEAD/Doc/examples/make_subsmat.py   biopython(Download)
from Bio import SubsMat
from Bio import AlignIO
from Bio.Alphabet import IUPAC, Gapped
from Bio.Align import AlignInfo
 
# get an alignment object from a Clustalw alignment output
c_align = AlignIO.read('protein.aln', 'clustal',
                       alphabet=Gapped(IUPAC.protein))

src/b/i/biopython-HEAD/Doc/examples/clustal_run.py   biopython(Download)
 
# biopython
from Bio.Alphabet import Gapped, IUPAC
from Bio.Align.Applications import ClustalwCommandline
from Bio import AlignIO
# Parse the output
alignment = AlignIO.read("test.aln", "clustal",
                         alphabet=Gapped(IUPAC.unambiguous_dna))
 
print(alignment)

src/b/i/biopython-HEAD/Bio/CodonAlign/CodonAlphabet.py   biopython(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import IUPAC, Gapped, HasStopCodon, Alphabet, generic_dna
from Bio.Data.CodonTable import generic_by_id
 
        alpha = alphabet
        if gap:
            alpha = Gapped(alpha, gap_char=gap)
        if stop:
            alpha = HasStopCodon(alpha, stop_symbol=stop)

src/h/y/hy454-0.4.4/lib/hy454/_graph.py   hy454(Download)
from tempfile import mkstemp
 
from Bio.Alphabet import Gapped, HasStopCodon, _verify_alphabet
from Bio.Alphabet.IUPAC import (ambiguous_dna, ambiguous_rna,
        extended_protein, unambiguous_dna, unambiguous_rna)
 
 
_DNA_ALPHABET = Gapped(ambiguous_dna)
_RNA_ALPHABET = Gapped(ambiguous_rna)
_AMINO_ALPHABET = HasStopCodon(Gapped(extended_protein, gap_char=_GAP), stop_symbol=_STOP)
def _fix_ambigs(pwm, alphabet):
    mapper = {}
    killchars = _GAP
    # killchars ambigs by distributing their probability uniformly 
    if alphabet == _DNA_ALPHABET or alphabet == _RNA_ALPHABET:

src/b/i/biopython-1.63/Bio/SeqIO/AceIO.py   biopython(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_nucleotide, generic_dna, generic_rna, Gapped
from Bio.Sequencing import Ace
 
            assert "-" not in consensus_seq_str
            consensus_seq = Seq(consensus_seq_str.replace("*", "-"),
                                Gapped(alpha, gap_char="-"))
        else:
            consensus_seq = Seq(consensus_seq_str, alpha)

src/b/i/biopython-HEAD/Bio/SeqIO/AceIO.py   biopython(Download)
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Alphabet import generic_nucleotide, generic_dna, generic_rna, Gapped
from Bio.Sequencing import Ace
 
            assert "-" not in consensus_seq_str
            consensus_seq = Seq(consensus_seq_str.replace("*", "-"),
                                Gapped(alpha, gap_char="-"))
        else:
            consensus_seq = Seq(consensus_seq_str, alpha)

src/b/i/biopython-1.63/Bio/Align/AlignInfo.py   biopython(Download)
    print("Trying a protein sequence with gaps and stops")
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py   biopython(Download)
    print("Trying a protein sequence with gaps and stops")
 
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")

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