minorg.extend_reference module

class minorg.extend_reference.UserAnnotation(ID, molecule, feature, parent=None, attr_mod={})[source]

Bases: object

__init__(ID, molecule, feature, parent=None, attr_mod={})[source]

generate_attr()[source]

generate_bed()[source]

generate_gff()[source]

generate_str(fmt='GFF')[source]

set_phase(seq)[source]

Set phase.

Accepts sequences of CDS up to self._start and counts number of non-gap characters to determine phase of current CDS feature.

Parameters: seq (str or Biopython Seq.Seq) – CDS sequence up to self._start

set_range(start, end)[source]: 0-index, start inclusive, end exclusive

minorg.extend_reference.aln_to_annotation(directory, fout, sep='.', outfmt='GFF', attr_mod=None, verbose=True)[source]

minorg.extend_reference.extend_reference(feature: list, subfeature: list, fout_fasta, fout_gff, mafft='mafft', feature_type='mRNA', subfeature_type='CDS', thread: int = 1, directory=None, tmp=True, logger=None)[source]

minorg.extend_reference.extend_reference_cli(args, config)[source]

minorg.extend_reference.extract_annotation(fa_aln, sep='.', attr_mod={})[source]

minorg.extend_reference.get_recursively(d, default, *keys)[source]

minorg.extend_reference.group_by_gene(fa_cds, fa_genomic, directory, sep='.', verbose=True, logger=None)[source]