Package Bio :: Package Phylo :: Package PAML :: Module _parse_codeml
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Module _parse_codeml

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Functions [hide private]
 
parse_basics(lines, results)
Parse the basic information that should be present in most codeml output files.
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parse_nssites(lines, results, multi_models, multi_genes)
Determine which NSsites models are present and parse them.
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parse_model(lines, results)
Parse an individual NSsites model's results.
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parse_siteclass_proportions(line_floats)
For models which have multiple site classes, find the proportion of the alignment assigned to each class.
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parse_siteclass_omegas(line, site_classes)
For models which have multiple site classes, find the omega estimated for each class.
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parse_clademodelc(branch_type_no, line_floats, site_classes)
Parse results specific to the clade model C.
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parse_branch_site_a(foreground, line_floats, site_classes)
Parse results specific to the branch site A model.
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parse_pairwise(lines, results)
Parse results from pairwise comparisons.
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parse_distances(lines, results)
Parse amino acid sequence distance results.
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Variables [hide private]
  line_floats_re = re.compile(r'-*\d+\.\d+')
  __package__ = 'Bio.Phylo.PAML'