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python-biopython  1.60
Classes | Functions | Variables
Bio.Align.AlignInfo Namespace Reference

Classes

class  SummaryInfo
class  PSSM

Functions

def print_info_content

Variables

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

Detailed Description

Extract information from alignment objects.

In order to try and avoid huge alignment objects with tons of functions,
functions which return summary type information about alignments should
be put into classes in this module.

classes:
o SummaryInfo
o PSSM

Function Documentation

def Bio.Align.AlignInfo.print_info_content (   summary_info,
  fout = None,
  rep_record = 0 
)
Three column output: position, aa in representative sequence,
    ic_vector value

Definition at line 674 of file AlignInfo.py.

00674 
00675 def print_info_content(summary_info,fout=None,rep_record=0):
00676     """ Three column output: position, aa in representative sequence,
00677         ic_vector value"""
00678     fout = fout or sys.stdout
00679     if not summary_info.ic_vector:
00680         summary_info.information_content()
00681     rep_sequence = summary_info.alignment._records[rep_record].seq
00682     positions = summary_info.ic_vector.keys()
00683     positions.sort()
00684     for pos in positions:
00685         fout.write("%d %s %.3f\n" % (pos, rep_sequence[pos],
00686                    summary_info.ic_vector[pos]))


Variable Documentation

Definition at line 720 of file AlignInfo.py.

Definition at line 698 of file AlignInfo.py.

Definition at line 719 of file AlignInfo.py.

Definition at line 710 of file AlignInfo.py.

tuple Bio.Align.AlignInfo.c = s.dumb_consensus(ambiguous="X")

Definition at line 728 of file AlignInfo.py.

Definition at line 715 of file AlignInfo.py.

tuple Bio.Align.AlignInfo.consensus = summary.dumb_consensus(ambiguous="N")

Definition at line 704 of file AlignInfo.py.

Initial value:
00001 FreqTable.FreqTable({"A":0.25,"G":0.25,"T":0.25,"C":0.25},
00002                                    FreqTable.FREQ,
00003                                    IUPAC.unambiguous_dna)

Definition at line 694 of file AlignInfo.py.

string Bio.Align.AlignInfo.filename = "../../Tests/GFF/multi.fna"

Definition at line 692 of file AlignInfo.py.

string Bio.Align.AlignInfo.format = "fasta"

Definition at line 693 of file AlignInfo.py.

Definition at line 25 of file AlignInfo.py.

Definition at line 24 of file AlignInfo.py.

Definition at line 727 of file AlignInfo.py.

Definition at line 703 of file AlignInfo.py.