Takes SeqRecordExpanded objects and creates datasets for phylogenetic software
Project description
Dataset creator for phylogenetic software
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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.x.x (2015-xx-xx)
It will not 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
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.
Project details
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