def __init__(self, file,fastaRecord): super(SequenceStat, self).__init__() self.file = file self.length = len(fastaRecord.seq) self.description=fastaRecord.description self.gc=SeqUtils.GC(fastaRecord.seq) self.crc32=CheckSum.crc32(fastaRecord.seq)
def __init__(self, file, fastaRecord):
super(SequenceStat, self).__init__()
self.file = file
self.length = len(fastaRecord.seq)
self.description = fastaRecord.description
self.gc = SeqUtils.GC(fastaRecord.seq)
self.crc32 = CheckSum.crc32(fastaRecord.seq)
print IUPACData.ambiguous_dna_complement #dictionary of complements
#and a lot more
from Bio.Data import CodonTable
print CodonTable.generic_by_id[2]
#SeqUtils. Several functions to deal with DNA and protein sequences.
#DNA utils
import Bio.SeqUtils as SeqUtils
print SeqUtils.GC('gacgatcggtattcgtag') #GC content
from Bio.SeqUtils import MeltingTemp
print MeltingTemp.Tm_staluc('tgcagtacgtatcgt') #DNA/RNA melting temperature
#checksum functions: short alphanumeric string signature of a file or sequence
#usually written in description of sequence
#cgc is a easy, weak, very used checksum (better crc32, crc64)
from Bio.SeqUtils import CheckSum
myseq='acaagatgccattgtcccccggcctcctgctgctgct'
print CheckSum.gcg(myseq)
print CheckSum.crc32(myseq)
print CheckSum.crc64(myseq)
print CheckSum.seguid(myseq)
#Protein utils
from Bio.SeqUtils import ProtParam
myprot=ProtParam.ProteinAnalysis('MLTNK')
print myprot.count_amino_acids()
print myprot.get_amino_acids_percent()
print myprot.molecular_weight()
print myprot.aromaticity()
print myprot.instability_index()
print myprot.flexibility()
print myprot.isoelectric_point()
print myprot.secondary_structure_fraction()