dataset-creator 0.3.3

Takes SeqRecordExpanded objects and creates datasets for phylogenetic software

Dataset creator for phylogenetic software

tests
package

Takes SeqRecordExpanded objects and creates datasets for phylogenetic software

• Free software: BSD license

Installation

pip install dataset_creator

Usage

The list of SeqRecordExpanded objects should be sorted by gene_code first then by voucher_code.

>>> from seqrecord_expanded import SeqRecord
>>> from dataset_creator import Dataset
>>>
>>> # `table` is the Translation Table code based on NCBI
>>> seq_record1 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='RpS5',
...                         table=1, voucher_code='CP100-10',
...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
>>>
>>> seq_record2 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='RpS5',
...                         table=1, voucher_code='CP100-10',
...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
>>>
>>> seq_record3 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='wingless',
...                         table=1, voucher_code='CP100-10',
...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
>>>
>>> seq_record4 = SeqRecord('ACTACCTA', reading_frame=2, gene_code='winglesss',
...                         table=1, voucher_code='CP100-10',
...                         taxonomy={'genus': 'Aus', 'species': 'bus'})
>>>
>>> seq_records = [
...    seq_record1, seq_record2, seq_record3, seq_record4,
... ]
>>> # codon positions can be 1st, 2nd, 3rd, 1st-2nd, ALL (default)
>>> dataset = Dataset(seq_records, format='NEXUS', partitioning='by gene',
...                   codon_positions='1st',
...                   )
>>> print(dataset.dataset_str)
"""#NEXUS
blah blah
"""

Development

To run the all tests run:

tox

Changelog

0.3.3 (2015-10-02)

• Fixed bug that raised an exception when SeqExpandedRecords did not have data in the taxonomy field.

0.3.2 (2015-10-01)

• Fixed bug that raised an exception when user wanted partitioned dataset as 1st-2nd and 3rd codon positions of only one codon.

0.3.1 (2015-10-01)

• Fixed bug that raised an exception when user wanted partitioned dataset by codon positions of only one codon.

0.3.0 (2015-10-01)

• Accepts voucher code as string that will be used to generate the outgroup string needed for NEXUS and TNT files.

0.2.0 (2015-09-30)

• Creates datasets as degenerated sequences using the method by Zwick et al.

0.1.1 (2015-09-30)

• It will issue errors if reading frames are not specified unless they are strictly necessary to build the dataset (datasets need to be divided by codon positions).

• Added documentation using sphinx-doc

• Creates datasets as aminoacid sequences.

0.1.0 (2015-09-23)

• Creates Nexus, Tnt, Fasta, Phylip and Mega dataset formats.

0.0.1 (2015-06-10)

• First release on PyPI.