Back to index

python-biopython  1.60
Classes | Namespaces | Functions | Variables
AlignInfo.py File Reference

Go to the source code of this file.

Classes

class  Bio.Align.AlignInfo.SummaryInfo
class  Bio.Align.AlignInfo.PSSM

Namespaces

namespace  Bio.Align.AlignInfo

Functions

def Bio.Align.AlignInfo.print_info_content

Variables

float Bio.Align.AlignInfo.Protein20Random = 0.05
float Bio.Align.AlignInfo.Nucleotide4Random = 0.25
string Bio.Align.AlignInfo.filename = "../../Tests/GFF/multi.fna"
string Bio.Align.AlignInfo.format = "fasta"
tuple Bio.Align.AlignInfo.expected
tuple Bio.Align.AlignInfo.alignment = AlignIO.read(open(filename), format)
tuple Bio.Align.AlignInfo.summary = SummaryInfo(alignment)
tuple Bio.Align.AlignInfo.consensus = summary.dumb_consensus(ambiguous="N")
 Bio.Align.AlignInfo.axis_seq = consensus)
list Bio.Align.AlignInfo.chars_to_ignore = ['-']
tuple Bio.Align.AlignInfo.alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
tuple Bio.Align.AlignInfo.a = Alignment(alpha)
tuple Bio.Align.AlignInfo.s = SummaryInfo(a)
tuple Bio.Align.AlignInfo.c = s.dumb_consensus(ambiguous="X")