biopython

v1.71.0

biopython v1.71.0 Bio.Nexus.Nexus

Nexus class. Parse the contents of a NEXUS file.

Based upon ‘NEXUS: An extensible file format for systematic information’ Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621

Link to this section Summary

Functions

_adjust_lines()

Adjust linebreaks to match ‘;’, strip leading/trailing whitespace

_compact4nexus()

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()

Delete []-delimited comments out of a file and break into lines separated by ‘;’

_make_unique()

Check that all values in list are unique and return a pruned and sorted list

_replace_parenthesized_ambigs()

Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code

_seqmatrix2strmatrix()

Converts a Seq-object matrix to a plain sequence-string matrix

_sort_keys_by_values()

Returns a sorted list of keys of p sorted by values of p

_unique_label()

Returns a unique name if label is already in previous_labels

combine()

Combine matrices in [(name,nexus-instance),…] and return new nexus instance

get_start_end()

Return position of first and last character which is not in skiplist

quotestrip()

Remove quotes and/or double quotes around identifiers

safename()

Return a taxon identifier according to NEXUS standard

Link to this section Functions

Link to this function _adjust_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)

Link to this function _compact4nexus()

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.).

Link to this function _kill_comments_and_break_lines()

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

Link to this function _make_unique()

Check that all values in list are unique and return a pruned and sorted list.

Link to this function _replace_parenthesized_ambigs()

Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code.

Link to this function _seqmatrix2strmatrix()

Converts a Seq-object matrix to a plain sequence-string matrix.

Link to this function _sort_keys_by_values()

Returns a sorted list of keys of p sorted by values of p.

Link to this function _unique_label()

Returns a unique name if label is already in previous_labels.

Link to this function combine()

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.

Link to this function get_start_end()

Return position of first and last character which is not in skiplist.

Skiplist defaults to [‘-‘,’?’].

Link to this function quotestrip()

Remove quotes and/or double quotes around identifiers.

Link to this function safename()

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 the mrbayes software package.