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Package Bio :: Package Nexus :: Module Nexus |
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Classes | |
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Block |
Represent a NEXUS block with block name and list of commandlines . |
CharBuffer |
Helps reading NEXUS-words and characters from a buffer. |
Commandline |
Represent a commandline as command and options. |
Nexus |
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StepMatrix |
Calculate a stepmatrix for weighted parsimony. |
Exceptions | |
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NexusError |
Function Summary | |
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Combine matrices in [(name,nexus-instance),...] and return new nexus instance. | |
Return position of first and last character which is not in skiplist (defaults to ['-','?']). | |
Remove quotes and/or double quotes around identifiers. | |
Return a taxon identifier according to NEXUS standard. |
Variable Summary | |
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str |
CHARSET = 'chars'
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int |
INTERLEAVE = 70 |
list |
KNOWN_NEXUS_BLOCKS = ['trees', 'data', 'characters', 'ta...
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str |
MRBAYESSAFE = 'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNO...
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str |
PUNCTUATION = '()[]{}/\\,;:=*\'"`+-<>'
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list |
SPECIAL_COMMANDS = ['charstatelabels', 'charlabels', 'ta...
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str |
TAXSET = 'taxa'
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str |
WHITESPACE = ' \t\n'
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Function Details |
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combine(matrices)Combine matrices in [(name,nexus-instance),...] and return new nexus instance. combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix. |
get_start_end(sequence, skiplist=['-', '?'])Return position of first and last character which is not in skiplist (defaults to ['-','?']). |
quotestrip(word)Remove quotes and/or double quotes around identifiers. |
safename(name, mrbayes=False)Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for mrbayes. |
Variable Details |
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CHARSET
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INTERLEAVE
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KNOWN_NEXUS_BLOCKS
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MRBAYESSAFE
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PUNCTUATION
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SPECIAL_COMMANDS
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TAXSET
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WHITESPACE
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