BioPython's SeqRecord class, but expanded with additional methods: degenerate seqs, codon positions based on reading frames, etc.
Project description
seqrecord-expanded
BioPython’s SeqRecord class, but expanded with additional methods: degenerate seqs, codon positions based on reading frames, etc.
Usage
By default it assumes a DNA sequence with ambiguous characters.
>>> from seqrecord_expanded import SeqRecordExpanded
>>> seq_record = SeqRecordExpanded('TCTGAATGGAAGACAAAGCGTCCA',
... voucher_code='CP100-09',
... taxonomy={'genus': 'Melitaea',
... 'species': 'phoebe',
... },
... gene_code='EF1a',
... reading_frame=1,
... table=1, # translation table
... )
>>> # Degenerate sequence standard genetic code
>>> seq_record.degenerate()
'TCNGARTGGAARACNAARMGNCCN'
>>>
>>> # Degenerate sequence S method
>>> seq_record.degenerate(method='S')
'AGYGARTGGAARACNAARMGNCCN'
>>>
>>> # Degenerate sequence Z method
>>> seq_record.degenerate(method='Z')
'TCNGARTGGAARACNAARMGNCCN'
>>>
>>> # Degenerate sequence SZ method
>>> seq_record.degenerate(method='SZ')
'NNNGARTGGAARACNAARMGNCCN'
>>>
>>> # get first codon positions
>>> seq_record.first_codon_position()
'TGTAAACC'
>>>
>>> # get second codon positions
>>> seq_record.second_codon_position()
'CAGACAGC'
>>>
>>> # get third codon positions
>>> seq_record.third_codon_position()
'TAGGAGTA'
>>>
>>> # get first and second positions
>>> seq_record.first_and_second_positions()
'TCGATGAAACAACGCC'
>>>
>>> # translate
>>> seq_record.translate()
OKPDOR
Installation
pip install seqrecord-expanded
Requirements
Python3.
pip install -r requirements.txt
Compatibility
Licence
BSD.
Project details
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