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Commit c9f01919 authored by Blaise Li's avatar Blaise Li
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Add brief importable default methods description.

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...@@ -3,5 +3,6 @@ __licence__ = "GNU GPLv3" ...@@ -3,5 +3,6 @@ __licence__ = "GNU GPLv3"
__version__ = 0.1 __version__ = 0.1
from .libconsensus import ( from .libconsensus import (
ali2cons, ali2cons,
default_cons_methods,
fasta2cons, fasta2cons,
) )
...@@ -106,6 +106,15 @@ def counts_add(cumul_counts, counter_item): ...@@ -106,6 +106,15 @@ def counts_add(cumul_counts, counter_item):
return cumul_counts[1] + counter_item[1] return cumul_counts[1] + counter_item[1]
# This should be updated if `col_consensus` changes.
default_cons_methods = """
A consensus of the aligned sequences was computed using a rather conservative approach:
If one nucleotide accounted for at least 75% of an alignment column, this column was represented by this nucleotide.
Otherwise, the "N" ambiguity code was used.
"""
def col_consensus(column, cum_freq=0.75, do_iupac=False): def col_consensus(column, cum_freq=0.75, do_iupac=False):
""" """
Determine the consensus of the letters present in *column*. Determine the consensus of the letters present in *column*.
......
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