biotaphy.common.data_readers

Module containing tools for reading alignment files in various formats.

Module Contents

Functions

create_sequence_list_from_dict(values_dict)	Creates a list of sequences from a dictionary.
get_character_matrix_from_sequences_list(sequences, var_headers=None)	Converts a list of sequences into a character matrix.
load_alignment_from_filename(filename)	Attempts to load an alignment from a file path by guessing schema.
read_csv_alignment_flo(csv_flo)	Reads a CSV file-like object and return a list of sequences and headers.
read_json_alignment_flo(json_flo)	Read a JSON file-like object and return a list of sequences and headers.
read_phylip_alignment_flo(phylip_flo)	Reads a phylip alignment file-like object and return the sequences.
read_table_alignment_flo(table_flo)	Reads a table from a file-like object.

exception biotaphy.common.data_readers.AlignmentIOError

Bases: Exception

Initialize self. See help(type(self)) for accurate signature.

biotaphy.common.data_readers.create_sequence_list_from_dict(values_dict)

Creates a list of sequences from a dictionary.

Parameters

values_dict (dict) – A dictionary of taxon name keys and a list of values for each value.

Note

• The dictionary should have structure:

  {
      "{taxon_name}" : [{values}]
  }
  

Returns

A list of Sequence objects and None for headers.

Return type

list

Raises

AlignmentIOError – If a dictionary value is not a list.

biotaphy.common.data_readers.get_character_matrix_from_sequences_list(sequences, var_headers=None)

Converts a list of sequences into a character matrix.

Parameters

• sequences (list of Sequence) – A list of Sequence objects to be converted.

• var_headers (list of headers, optional) – If provided, uses these as variable headers for the columns in the matrix.

Returns

A matrix of sequence data.

Return type

Matrix

biotaphy.common.data_readers.load_alignment_from_filename(filename)

Attempts to load an alignment from a file path by guessing schema.

Parameters

filename (str) – The file location containing the alignment

Raises

RuntimeError – Raised with the method needed to load the alignment cannot be determined.

Returns

Containing a list of sequences and headers

Return type

tuple

biotaphy.common.data_readers.read_csv_alignment_flo(csv_flo)

Reads a CSV file-like object and return a list of sequences and headers.

Parameters

csv_flo (file-like) – A file-like object with CSV alignment data.

Returns

A list of Sequence objects and headers.

Raises

AlignmentIOError – If the number of columns is inconsistent across the sequences.

biotaphy.common.data_readers.read_json_alignment_flo(json_flo)

Read a JSON file-like object and return a list of sequences and headers.

Parameters

json_flo (file-like) – A file-like object with JSON alignment data.

Note

• File should have structure:

  {
      "headers" : [{header_names}],
      "values" : [
          {
              "name" : "{taxon_name}",
              "values" : [{values}]
          }
      ]
  }
  

Returns

A list of Sequence objects and headers.

Raises

AlignmentIOError – If headers are provided but they are not a list.

biotaphy.common.data_readers.read_phylip_alignment_flo(phylip_flo)

Reads a phylip alignment file-like object and return the sequences.

Parameters

phylip_flo (file-like) – The phylip file-like object.

Note

• We assume that the phylip files are extended and not strict (in terms

  of how many characters for taxon names).

• The phylip file is in the format::

  numoftaxa numofsites seqlabel sequence seqlabel sequence

Returns

A list of Sequence objects.

Raises

AlignmentIOError – If there is a problem creating sequences.

biotaphy.common.data_readers.read_table_alignment_flo(table_flo)

Reads a table from a file-like object.

Parameters

table_flo (file-like) – A file-like object containing table data.

Returns

A list of Sequence objects.

Raises

AlignmentIOError – If there is a problem creating sequences.