Interfaces define functions that enable the reading or writing of data into or out of SHEPHARD proteomes. In particular, these functions operate by taking a Proteome object and then either annotating the proteins in that Proteome object with Tracks, Domains, Sites, or Attributes, OR writing Tracks, Domains, Sites or Attributes to file.
By way of a simple example, here we use the Domains interface package.
from shephard.apis import fasta
from shephard import interfaces
# create a new Proteome from a FASTA file
small_proteom = fasta.fasta_to_proteome('sequences.fasta')
# use the interfaces package to annotate the Proteome object with the domains
# in the file `DNA_binding_domains.tsv`
interfaces.si_domains.add_domains_from_file(small_proteom, 'DNA_binding_domains.tsv')By using interfaces, we ensure that, as long as you can write your data in a format that complies with a Track, Site, Domain, or Protein_attribute file, you can be sure it will be correctly read into SHEPHARD and is then accessible within the larger framework.
Functions associated with the si_sites module enable the reading and writing of SHEPHARD Sites files.
shephard.interfaces.si_sites.add_sites_from_file
shephard.interfaces.si_sites.add_sites_from_dictionary
shephard.interfaces.si_sites.write_sites
shephard.interfaces.si_sites.write_sites_from_list
Functions associated with the si_domains module enable the reading and writing of SHEPHARD Domains files.
shephard.interfaces.si_domains.add_domains_from_file
shephard.interfaces.si_domains.add_domains_from_dictionary
shephard.interfaces.si_domains.add_domain_attributes_from_file
shephard.interfaces.si_domains.add_domain_attributes_from_dictionary
shephard.interfaces.si_domains.write_domains
shephard.interfaces.si_domains.write_domains_from_list
Functions associated with the si_tracks module enable the reading and writing of SHEPHARD Tracks files.
shephard.interfaces.si_tracks.add_tracks_from_dictionary
shephard.interfaces.si_tracks.add_tracks_from_file
shephard.interfaces.si_tracks.write_all_tracks_separate_files
shephard.interfaces.si_tracks.write_all_values_tracks_single_file
shephard.interfaces.si_tracks.write_all_symbols_tracks_single_file
shephard.interfaces.si_tracks.write_tracks
shephard.interfaces.si_tracks.write_tracks_from_list
Functions associated with the si_protein_attributes module enable the reading and writing of SHEPHARD Protein attribute files.
shephard.interfaces.si_protein_attributes.add_protein_attributes_from_dictionary
shephard.interfaces.si_protein_attributes.add_protein_attributes_from_file
shephard.interfaces.si_protein_attributes.write_protein_attributes
Functions associated with the si_protein_attributes module enable the reading and writing of SHEPHARD Protein files. While we include this for completeness, our general recommendation is to use FASTA files for protein information, and then write protein attributes out as separate protein attributes files. The reason for this is that this ensures easy readability of both protein sequence information and protein annotation information.
shephard.interfaces.si_proteins.add_proteins_from_dictionary
shephard.interfaces.si_proteins.add_proteins_from_file
shephard.interfaces.si_proteins.write_proteins