Protein Sequences
Handle proteins for the picked protein FDR.
- class mokapot.proteins.Proteins(decoy_prefix, peptide_map, protein_map, shared_peptides, has_decoys)[source]
Store protein sequences.
This class stores the mapping of peptides to proteins and the mapping of target proteins to their corresponding decoy proteins.
We recommend creating Proteins objects using the
mokapot.read_fasta()function.- Parameters:
- decoy_prefixstr
The prefix used to indicate a decoy protein in the description lines of the FASTA file.
- peptide_mapDict[str, str]
A dictionary mapping peptide sequences to the proteins that may have generated them.
- protein_mapDict[str, str]
A dictionary mapping decoy proteins to the target proteins from which they were generated.
- shared_peptidesDict[str]
A dictionary mapping shared peptides to the proteins that may have generated them.
- has_decoysbool
Did the FASTA file have decoy proteins in it?
- Attributes:
- decoy_prefixstr
The prefix used to indicate a decoy protein in the description lines of the FASTA file.
- peptide_mapDict[str, str]
A dictionary mapping peptide sequences to the proteins that may have generated them.
- protein_mapDict[str, str]
A dictionary mapping decoy proteins to the target proteins from which they were generated.
- shared_peptidesDict[str]
A dictionary mapping shared peptides to the proteins that may have generated them.
- has_decoysbool
Did the FASTA file have decoy proteins in it?