Command Line Interface Reference

teiphy

teiphy [OPTIONS] INPUT OUTPUT

Options

-t <trivial_reading_types>

Reading types to treat as trivial and collapse with the previous substantive reading (e.g., reconstructed, defective, orthographic, subreading). If more than one type is applicable, this argument can be specified multiple times.

Default:

-m <missing_reading_types>

Reading types to treat as missing data (e.g., lac, overlap). If more than one type is applicable, this argument can be specified multiple times.

Default:

-s <suffixes>

Suffixes to ignore for manuscript witness sigla. Typically, these will be things like the sigla for first hands (*) and main texts (T), although you may also wish to use it to combine multiple attestations (often signified by /1, /2 in lectionaries) in the same witness. If more than one suffix is used, this argument can be specified multiple times.

Default:

--fill-correctors, --no-fill-correctors

Fill in missing readings in witnesses with type “corrector” using the witnesses they follow in the TEI XML witness list.

Default:

False

--labels, --no-labels

Print the CharStateLabels block (containing variation unit labels and reading texts converted to ASCII) in NEXUS output.

Default:

True

--frequency, --no-frequency

Use the StatesFormat=Frequency setting instead of the StatesFormat=StatesPresent setting (and thus represent all states with frequency vectors rather than symbols) in NEXUS output.

Default:

False

--fragmentary-threshold <fragmentary_threshold>

Ignore all witnesses that are extant at fewer than the specified proportion of variation units. For the purposes of this calculation, a witness is considered non-extant/lacunose at a variation unit if the type of its reading in that unit is in the user-specified list of missing reading types (i.e., the argument(s) of the -m option). This calculation is performed after the reading sequences of correctors have been filled in (if the –fill-correctors flag was specified). Thus, a threshold of 0.7 means that a witness with missing readings at more than 30 percent of variation units will be excluded from the output.

--drop-constant, --no-drop-constant

If set, do not write constant sites (i.e., variation units with one substantive reading) to output.

Default:

False

--ambiguous-as-missing, --no-ambiguous-as-missing

Use the missing symbol instead of multistate symbols (and thus treat all ambiguities as missing data) in NEXUS output; this option is only applied if the –frequency option is not set.

Default:

False

--proportion, --no-proportion

If set, populate the output distance matrix’s cells with proportions of disagreements over variation units where both witnesses are extant; this option is only used if –table distance is specified.

Default:

False

--calibrate-dates, --no-calibrate-dates

Add an Assumptions block containing age distributions for witnesses to NEXUS output; this option is intended for NEXUS inputs to BEAST 2.

Default:

False

--mrbayes, --no-mrbayes

Add a MrBayes block containing model settings and age calibrations for witnesses to NEXUS output; this option is intended for inputs to MrBayes.

Default:

False

--clock <clock>

The clock model to use; this option is intended for inputs to MrBayes and BEAST 2. MrBayes does not presently support a local clock model, so it will default to a strict clock model if a local clock model is specified.

Default:

ClockModel.strict

Options:

strict | uncorrelated | local

--ancestral-logger <ancestral_logger>

The type of logger to use for ancestral state reconstruction data; this option is intended for inputs to BEAST 2. If “state”, then only the reconstructed states at the root of each sampled tree will be logged. If “sequence”, then each sampled tree’s reconstructed states for all ancestors will be logged (WARNING: this will be memory-intensive!). If “none”, then no ancestral states will be logged.

Default:

AncestralLogger.state

Options:

state | sequence | none

--table <table>

The type of table to use for CSV/Excel output. If “matrix”, then the table will have rows for witnesses and columns for all variant readings, with frequency values in cells (the –split-missing flag can be used with this option). If “distance”, then the table will have rows and columns for witnesses, with the number or proportion of disagreements between each pair in the corresponding cell (the –proportion flag can be used with this option). If “similarity”, then the table will have rows and columns for witnesses, with the number or proportion of agreements between each pair in the corresponding cell (the –proportion flag can be used with this option). If “nexus”, then the table will have rows for witnesses and columns for variation units with reading IDs in cells (the –ambiguous-as-missing flag can be used with this option). If “long”, then the table will consist of repeated rows with column entries for taxa, characters, reading indices, and reading texts.

Default:

TableType.matrix

Options:

matrix | distance | similarity | nexus | long

--split-missing, --no-split-missing

Treat missing characters/variation units as having a contribution of 1 split over all states/readings; if False, then missing data is ignored (i.e., all states are 0). Not applicable for non-tabular formats.

Default:

False

--show-ext, --no-show-ext

If set, each cell in a distance or similarity matrix will display the count/proportion of disagreements/agreements, followed by the number of variation units where both witnesses are extant and have unambiguous readings. (For example, a cell containing 47/50 in a similarity table would indicate that the row and column witnesses agree at 47 of the 50 units where they both have readings.) This option is only valid for tabular output formats of type “distance” or “similarity”.

Default:

False

--seed <seed>

Seed for random number generation (used for setting default initial values of transcriptional rate parameters for BEAST 2 XML output); if not specified, then the default seeding of the numpy.random.default_rng class will be used.

--verbose, --no-verbose

Enable verbose logging (mostly for debugging purposes).

Default:

False

--version, --no-version

Print the current version.

Default:

False

--format <format>

The output format.

Options:

NEXUS | HENNIG86 | PHYLIP | FASTA | BEAST | CSV | TSV | EXCEL | STEMMA

--dates-file <dates_file>

CSV file containing witness IDs in the first column and minimum and maximum dates for those witnesses in the next two columns. If specified, then for all witnesses in the first column, any existing date ranges for them in the TEI XML collation will be ignored.

--install-completion <install_completion>

Install completion for the specified shell.

Options:

bash | zsh | fish | powershell | pwsh

--show-completion <show_completion>

Show completion for the specified shell, to copy it or customize the installation.

Options:

bash | zsh | fish | powershell | pwsh

Arguments

INPUT

Required argument Input TEI XML collation file to convert. <click.types.Path object at 0x7fd8a919a280>

OUTPUT

Required argument Output for converted collation. If –format is not specified, then the format will be derived from the extension of this file. <click.types.Path object at 0x7fd8a919a310>