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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. | |
Adjust linebreaks to match ';', strip leading/trailing whitespace | |
Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class) into '2-4 6-9 13-19\3 21' (baseindex 1, used in programs like Paup or MrBayes.). | |
Delete []-delimited comments out of a file and break into lines separated by ';'. | |
Check that all values in list are unique and return a pruned and sorted list. | |
Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code. | |
Converts a Seq-object matrix to a plain sequence-string matrix. | |
Returns a sorted list of keys of p sorted by values of p. |
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. |
_adjust_lines(lines)Adjust linebreaks to match ';', strip leading/trailing whitespace list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so that no linebreaks occur within a commandline (except matrix command line) |
_compact4nexus(orig_list)Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class) into '2-4 6-9 13-19\3 21' (baseindex 1, used in programs like Paup or MrBayes.). |
_kill_comments_and_break_lines(text)Delete []-delimited comments out of a file and break into lines separated by ';'. stripped_text=_kill_comments_and_break_lines(text): Nested and multiline comments are allowed. [ and ] symbols within single or double quotes are ignored, newline ends a quote, all symbols with quotes are treated the same (thus not quoting inside comments like [this character ']' ends a comment]) Special [&...] and [\...] comments remain untouched, if not inside standard comment. Quotes inside special [& and [\ are treated as normal characters, but no nesting inside these special comments allowed (like [& [\ ]]). ';' ist deleted from end of line. NOTE: this function is very slow for large files, and obsolete when using C extension cnexus |
_make_unique(l)Check that all values in list are unique and return a pruned and sorted list. |
_replace_parenthesized_ambigs(seq, rev_ambig_values)Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code. |
_seqmatrix2strmatrix(matrix)Converts a Seq-object matrix to a plain sequence-string matrix. |
_sort_keys_by_values(p)Returns a sorted list of keys of p sorted by values of p. |
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