Package Bio :: Package Phylo :: Package PAML :: Module _parse_yn00
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Module _parse_yn00

source code

Functions [hide private]
 
parse_ng86(lines, results)
Parse the Nei & Gojobori (1986) section of the resuls.
source code
 
parse_yn00(lines, results, sequences)
Parse the Yang & Nielsen (2000) part of the results.
source code
 
parse_others(lines, results, sequences)
Parse the results from the other methods.
source code
Variables [hide private]
  __package__ = 'Bio.Phylo.PAML'
Function Details [hide private]

parse_ng86(lines, results)

source code 
Parse the Nei & Gojobori (1986) section of the resuls.
Nei_Gojobori results are organized in a lower
triangular mattrix, with the sequence names labeling
the rows and statistics in the format:
w (dN dS) per column
Example row (2 columns):
0.0000 (0.0000 0.0207) 0.0000 (0.0000 0.0421)

parse_yn00(lines, results, sequences)

source code 
Parse the Yang & Nielsen (2000) part of the results.
Yang & Nielsen results are organized in a table with
each row comprising one pairwise species comparison.
Rows are labeled by spequence number rather than by
sequence name.

parse_others(lines, results, sequences)

source code 
Parse the results from the other methods.

The remaining methods are grouped together. Statistics
for all three are listed for each of the pairwise
species comparisons, with each method's results on its
own line.
The stats in this section must be handled differently
due to the possible presence of NaN values, which won't
get caught by my typical "line_floats" method used above.