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All Samples(18)  |  Call(9)  |  Derive(0)  |  Import(9)
Calculates G+C content, returns the percentage (float between 0 and 100).

Copes mixed case sequences, and with the ambiguous nucleotide S (G or C)
when counting the G and C content.  The percentage is calculated against
the full length, e.g.:

>>> from Bio.SeqUtils import GC
>>> GC("ACTGN")
40.0
(more...)

        def GC(seq):
    """Calculates G+C content, returns the percentage (float between 0 and 100).

    Copes mixed case sequences, and with the ambiguous nucleotide S (G or C)
    when counting the G and C content.  The percentage is calculated against
    the full length, e.g.:

    >>> from Bio.SeqUtils import GC
    >>> GC("ACTGN")
    40.0

    Note that this will return zero for an empty sequence.
    """
    try:
        gc = sum(seq.count(x) for x in ['G', 'C', 'g', 'c', 'S', 's'])
        return gc*100.0/len(seq)
    except ZeroDivisionError:
        return 0.0
        


src/b/i/biopython-1.63/Scripts/xbbtools/xbb_translations.py   biopython(Download)
 
from Bio.Seq import reverse_complement, translate
from Bio.SeqUtils import GC
 
 
    def gc(self, seq):
        """Returns a float between 0 and 100."""
        return GC(seq)
 
    def gcframe(self, seq, translation_table=1):

src/b/i/biopython-HEAD/Scripts/xbbtools/xbb_translations.py   biopython(Download)
 
from Bio.Seq import reverse_complement, translate
from Bio.SeqUtils import GC
 
 
    def gc(self, seq):
        """Returns a float between 0 and 100."""
        return GC(seq)
 
    def gcframe(self, seq, translation_table=1):

src/p/y/pydna-0.6.1/pydna/amplify.py   pydna(Download)
from Bio.Alphabet.IUPAC             import ambiguous_dna
from Bio.SeqRecord                  import SeqRecord
from Bio.SeqUtils                   import GC
from Bio.SeqUtils.MeltingTemp       import Tm_staluc
from Bio.SeqFeature                 import SeqFeature
        # ing temperature for DNA amplification in vitro
        # http://www.ncbi.nlm.nih.gov/pubmed/2003928
        GC_prod=GC(str(self.seq))
        tml = min(self.tmf,self.tmr)
        #print GC(str(self.product.seq)), self.saltc/1000.0, len(self.product)
        tmp = 81.5 + 0.41*GC(str(self.seq)) + 16.6*log10(self.saltc/1000.0) - 675/len(self)

src/p/y/python-dna-0.1.2/pydna/amplify.py   python-dna(Download)
from Bio.Alphabet.IUPAC             import ambiguous_dna
from Bio.SeqRecord                  import SeqRecord
from Bio.SeqUtils                   import GC
from Bio.SeqUtils.MeltingTemp       import Tm_staluc
from Bio.SeqFeature                 import SeqFeature
        # ing temperature for DNA amplification in vitro
        # http://www.ncbi.nlm.nih.gov/pubmed/2003928
        GC_prod=GC(str(self.product.seq))
        tml = min(self.tmf,self.tmr)
        #print GC(str(self.product.seq)), self.saltc/1000.0, len(self.product)
        tmp = 81.5 + 0.41*GC(str(self.product.seq)) + 16.6*log10(self.saltc/1000.0) - 675/len(self.product)

src/c/o/CONCOCT-HEAD/scripts/evaluation/gen_input_table_taxonomy.py   CONCOCT(Download)
 
from Bio import SeqIO
from Bio.SeqUtils import GC
 
from BCBio import GFF
    for rec in SeqIO.parse(fastafile, "fasta"):
        out_dict[rec.id] = {}
        out_dict[rec.id]["GC"] = GC(rec.seq)
        out_dict[rec.id]["length"] = len(rec.seq)
 

src/m/i/misc-genomics-tools-HEAD/scripts/spades_to_blobology.py   misc-genomics-tools(Download)
 
from Bio import SeqIO
from Bio.SeqUtils import GC
import sys
 
def contig_stat(fn, rec):
	cols = rec.id.split("_")
	return "%s\t%s\t%s\t%s\t%s" % (fn, rec.id, len(rec), GC(rec.seq), cols[5])

src/m/i/MIX-HEAD/bin/fasta_statistics.py   MIX(Download)
		self.length = len(fastaRecord.seq)
		self.description=fastaRecord.description
		self.gc=SeqUtils.GC(fastaRecord.seq)
		self.crc32=CheckSum.crc32(fastaRecord.seq)
 

src/p/y/pydna-0.6.1/pydna/primer_design.py   pydna(Download)
'''
from operator import itemgetter
from Bio.SeqUtils import GC
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord

src/b/i/biopython-HEAD/Tests/test_SeqUtils.py   biopython(Download)
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils import GC, seq1, seq3
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid

src/b/i/biopython-1.63/Tests/test_SeqUtils.py   biopython(Download)
from Bio.Seq import Seq, MutableSeq
from Bio.SeqRecord import SeqRecord
from Bio.SeqUtils import GC, quick_FASTA_reader, seq1, seq3
from Bio.SeqUtils.lcc import lcc_simp, lcc_mult
from Bio.SeqUtils.CheckSum import crc32, crc64, gcg, seguid