def get_column(self, col):
"""Returns a string containing a given column (DEPRECATED).
This is a method provided for backwards compatibility with the old
Bio.Align.Generic.Alignment object. Please use the slice notation
instead, since get_column is likely to be removed in a future release
of Biopython..
"""
import warnings
import Bio
warnings.warn("This method is deprecated and is provided for backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the slice notation instead, as get_column is likely to be removed in a future release of Biopython.", Bio.BiopythonDeprecationWarning)
return _Alignment.get_column(self, col)
def get_column(self, col):
"""Returns a string containing a given column (DEPRECATED).
This is a method provided for backwards compatibility with the old
Bio.Align.Generic.Alignment object. Please use the slice notation
instead, since get_column is likely to be removed in a future release
of Biopython..
"""
import warnings
import Bio
warnings.warn(
"This method is deprecated and is provided for backwards compatibility with the old Bio.Align.Generic.Alignment object. Please use the slice notation instead, as get_column is likely to be removed in a future release of Biopython.",
Bio.BiopythonDeprecationWarning,
)
return _Alignment.get_column(self, col)
print(consensus)
consensus = summary.gap_consensus(ambiguous="N")
print(consensus)
print("")
print(summary.pos_specific_score_matrix(chars_to_ignore=['-'],
axis_seq=consensus))
print("")
#Have a generic alphabet, without a declared gap char, so must tell
#provide the frequencies and chars to ignore explicitly.
print(summary.information_content(e_freq_table=expected,
chars_to_ignore=['-']))
print("")
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-")
a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")
a.add_sequence("ID003", "MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*")
print(a)
print("="*a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
print(c)
c = s.gap_consensus(ambiguous="X")
print(c)
print("")
print(s.pos_specific_score_matrix(chars_to_ignore=['-', '*'], axis_seq=c))
print(s.information_content(chars_to_ignore=['-', '*']))
print("")
print(
summary.pos_specific_score_matrix(chars_to_ignore=['-'],
axis_seq=consensus))
print("")
#Have a generic alphabet, without a declared gap char, so must tell
#provide the frequencies and chars to ignore explicitly.
print(
summary.information_content(e_freq_table=expected,
chars_to_ignore=['-']))
print("")
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-")
a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")
a.add_sequence("ID003", "MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*")
print(a)
print("=" * a.get_alignment_length())
s = SummaryInfo(a)
c = s.dumb_consensus(ambiguous="X")
print(c)
c = s.gap_consensus(ambiguous="X")
print(c)
print("")
print(s.pos_specific_score_matrix(chars_to_ignore=['-', '*'], axis_seq=c))
print(s.information_content(chars_to_ignore=['-', '*']))