dataset-creator 0.1.0

Takes SeqRecordExpanded objects and creates datasets for phylogenetic software

tests
package

Takes SeqRecordExpanded objects and creates datasets for phylogenetic software

• Free software: BSD license

Installation

pip install dataset_creator

Usage

>>> 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_records = [
...    seq_record1, seq_record2,
... ]
>>> # 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

0.1.0 (2015-09-23)

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

0.0.1 (2015-06-10)

• First release on PyPI.