silvio.extensions.records.gene package¶

Submodules¶

silvio.extensions.records.gene.crafted_gene module¶

Gene crafted by the user itself.

class silvio.extensions.records.gene.crafted_gene.CraftedGene(name: str, orf: Bio.Seq.Seq, prom: Bio.Seq.Seq)[source]¶

Bases: silvio.extensions.records.gene.gene.Gene

_abc_impl = <_abc._abc_data object>¶

make_variant(orf_loc: int, orf_sub: Bio.Seq.Seq) → silvio.extensions.records.gene.crafted_gene.CraftedGene[source]¶: TODO: Maybe its better to clone-then-mutate.

name¶

orf¶

prom¶

silvio.extensions.records.gene.gene module¶

The Gene component stores the:

ORF and Promoter sequences (enhancers in future?)
a name as designation
(annotations in future - all that what biopython brings to the table)

class silvio.extensions.records.gene.gene.Gene[source]¶

Bases: silvio.record.Record, abc.ABC

_abc_impl = <_abc._abc_data object>¶

name¶

orf¶

prom¶

silvio.extensions.records.gene.localized_gene module¶

class silvio.extensions.records.gene.localized_gene.LocalizedGene(name: str, seq: Bio.Seq.Seq, start_loc: int, prom_len: int, orf_len: int)[source]¶

Bases: silvio.extensions.records.gene.gene.Gene

Gene that stores its sequence in a shared sequence.

TODO: Simple for now. Only has promoter and ORF which are adjacent to each other.

_abc_impl = <_abc._abc_data object>¶

end_loc¶

name¶

orf¶

orf_len¶

prom¶

prom_len¶

seq¶

start_loc¶

silvio.extensions.records.gene.stub_gene module¶

StubGene is a gene with no information about its actual sequence. It only has properties about its name.

class silvio.extensions.records.gene.stub_gene.StubGene(name: str)[source]¶

Bases: silvio.extensions.records.gene.gene.Gene

_abc_impl = <_abc._abc_data object>¶

name¶

orf¶

prom¶