Site curation and mapping (`indra.preassembler.sitemapper`)

class indra.preassembler.sitemapper.MappedStatement(original_stmt, mapped_mods, mapped_stmt)[source]

Information about a Statement found to have invalid sites.

Parameters

original_stmt (indra.statements.Statement) – The statement prior to mapping.
mapped_mods (list of MappedSite) – A list of MappedSite objects.
mapped_stmt (indra.statements.Statement) – The statement after mapping. Note that if no information was found in the site map, it will be identical to the original statement.

class indra.preassembler.sitemapper.SiteMapper(site_map=None, use_cache=False, cache_path=None, do_methionine_offset=True, do_orthology_mapping=True, do_isoform_mapping=True)[source]

Use site information to fix modification sites in Statements.

This is a wrapper around the protmapper package’s ProtMapper class and adds all the additional functionality to handle INDRA Statements and Agents.

Parameters

site_map (dict (as returned by load_site_map())) – A dict mapping tuples of the form (gene, orig_res, orig_pos) to a tuple of the form (correct_res, correct_pos, comment), where gene is the string name of the gene (canonicalized to HGNC); orig_res and orig_pos are the residue and position to be mapped; correct_res and correct_pos are the corrected residue and position, and comment is a string describing the reason for the mapping (species error, isoform error, wrong residue name, etc.).
use_cache (Optional[bool]) – If True, the SITEMAPPER_CACHE_PATH from the config (or environment) is loaded and cached mappings are read and written to the given path. Otherwise, no cache is used. Default: False
do_methionine_offset (boolean) – Whether to check for off-by-one errors in site position (possibly) attributable to site numbering from mature proteins after cleavage of the initial methionine. If True, checks the reference sequence for a known modification at 1 site position greater than the given one; if there exists such a site, creates the mapping. Default is True.
do_orthology_mapping (boolean) – Whether to check sequence positions for known modification sites in mouse or rat sequences (based on PhosphoSitePlus data). If a mouse/rat site is found that is linked to a site in the human reference sequence, a mapping is created. Default is True.
do_isoform_mapping (boolean) – Whether to check sequence positions for known modifications in other human isoforms of the protein (based on PhosphoSitePlus data). If a site is found that is linked to a site in the human reference sequence, a mapping is created. Default is True.

Examples

Fixing site errors on both the modification state of an agent (MAP2K1) and the target of a Phosphorylation statement (MAPK1):

>>> map2k1_phos = Agent('MAP2K1', db_refs={'UP':'Q02750'}, mods=[
... ModCondition('phosphorylation', 'S', '217'),
... ModCondition('phosphorylation', 'S', '221')])
>>> mapk1 = Agent('MAPK1', db_refs={'UP':'P28482'})
>>> stmt = Phosphorylation(map2k1_phos, mapk1, 'T','183')
>>> (valid, mapped) = default_mapper.map_sites([stmt])
>>> valid
[]
>>> mapped
[
MappedStatement:
    original_stmt: Phosphorylation(MAP2K1(mods: (phosphorylation, S, 217), (phosphorylation, S, 221)), MAPK1(), T, 183)
    mapped_mods: MappedSite(up_id='Q02750', error_code=None, valid=False, orig_res='S', orig_pos='217', mapped_id='Q02750', mapped_res='S', mapped_pos='218', description='off by one', gene_name='MAP2K1')
                 MappedSite(up_id='Q02750', error_code=None, valid=False, orig_res='S', orig_pos='221', mapped_id='Q02750', mapped_res='S', mapped_pos='222', description='off by one', gene_name='MAP2K1')
                 MappedSite(up_id='P28482', error_code=None, valid=False, orig_res='T', orig_pos='183', mapped_id='P28482', mapped_res='T', mapped_pos='185', description='INFERRED_MOUSE_SITE', gene_name='MAPK1')
    mapped_stmt: Phosphorylation(MAP2K1(mods: (phosphorylation, S, 218), (phosphorylation, S, 222)), MAPK1(), T, 185)
]
>>> ms = mapped[0]
>>> ms.original_stmt
Phosphorylation(MAP2K1(mods: (phosphorylation, S, 217), (phosphorylation, S, 221)), MAPK1(), T, 183)
>>> ms.mapped_mods
[MappedSite(up_id='Q02750', error_code=None, valid=False, orig_res='S', orig_pos='217', mapped_id='Q02750', mapped_res='S', mapped_pos='218', description='off by one', gene_name='MAP2K1'), MappedSite(up_id='Q02750', error_code=None, valid=False, orig_res='S', orig_pos='221', mapped_id='Q02750', mapped_res='S', mapped_pos='222', description='off by one', gene_name='MAP2K1'), MappedSite(up_id='P28482', error_code=None, valid=False, orig_res='T', orig_pos='183', mapped_id='P28482', mapped_res='T', mapped_pos='185', description='INFERRED_MOUSE_SITE', gene_name='MAPK1')]
>>> ms.mapped_stmt
Phosphorylation(MAP2K1(mods: (phosphorylation, S, 218), (phosphorylation, S, 222)), MAPK1(), T, 185)

map_sites(stmts)[source]

Check a set of statements for invalid modification sites.

Statements are checked against Uniprot reference sequences to determine if residues referred to by post-translational modifications exist at the given positions.

If there is nothing amiss with a statement (modifications on any of the agents, modifications made in the statement, etc.), then the statement goes into the list of valid statements. If there is a problem with the statement, the offending modifications are looked up in the site map (site_map), and an instance of MappedStatement is added to the list of mapped statements.

Parameters: stmts (list of indra.statement.Statement) – The statements to check for site errors.
Returns: 2-tuple containing (valid_statements, mapped_statements). The first element of the tuple is a list of valid statements (indra.statement.Statement) that were not found to contain any site errors. The second element of the tuple is a list of mapped statements (MappedStatement) with information on the incorrect sites and corresponding statements with correctly mapped sites.
Return type: tuple

Site curation and mapping (indra.preassembler.sitemapper)

Site curation and mapping (`indra.preassembler.sitemapper`)