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
0.3.8 (2015-10-30)
Fixed making dataset as aminoacid seqs for MEGA format.
Fixed making dataset as degenerated seqs for MEGA format.
Fixed making dataset as degenerated seqs for TNT format.
Fixed making dataset as aa seqs with specified outgroup for TNT format.
Raise ValueError when asked to degenerate seqs that will go to partitioning based on codon positions.
Dataset creator returns warnings if translated sequences have stop codons ‘*’.
Cannot generate MEGA datasets with partitioning.
0.3.7 (2015-10-30)
Fixed 2nd, 3rd codon positions bug that returned empty FASTA datasets.
0.3.6 (2015-10-30)
Fixed 3rd codon positions bug that returned FASTA datasets with 3rd codon positions even if they were not needed.
0.3.5 (2015-10-29)
If user provides outgroup, then TNT datasets will place its sequences in first position in the dataset blocks.
0.3.4 (2015-10-02)
Fixed bug that did not show DATATYPE=PROTEIN in Nexus files when aminoacid sequences were requested by user.
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.
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