PhosphoSite client¶

class protmapper.phosphosite_client.PhosphoSite(GENE, PROTEIN, ACC_ID, HU_CHR_LOC, MOD_RSD, SITE_GRP_ID, ORGANISM, MW_kD, DOMAIN, SITE_7_AA, LT_LIT, MS_LIT, MS_CST, CST_CAT)¶

Bases: tuple

ACC_ID¶: Alias for field number 2

CST_CAT¶: Alias for field number 13

DOMAIN¶: Alias for field number 8

GENE¶: Alias for field number 0

HU_CHR_LOC¶: Alias for field number 3

LT_LIT¶: Alias for field number 10

MOD_RSD¶: Alias for field number 4

MS_CST¶: Alias for field number 12

MS_LIT¶: Alias for field number 11

MW_kD¶: Alias for field number 7

ORGANISM¶: Alias for field number 6

PROTEIN¶: Alias for field number 1

SITE_7_AA¶: Alias for field number 9

SITE_GRP_ID¶: Alias for field number 5

class protmapper.phosphosite_client.PspMapping(mapped_id, mapped_res, mapped_pos, motif, respos)¶

Bases: tuple

mapped_id¶: Alias for field number 0

mapped_pos¶: Alias for field number 2

mapped_res¶: Alias for field number 1

motif¶: Alias for field number 3

respos¶: Alias for field number 4

protmapper.phosphosite_client.has_data()[source]¶

Check if the PhosphoSite data is available and can be loaded.

Returns:	True if the data can be loaded, False otherwise.
Return type:	bool

protmapper.phosphosite_client.map_to_human_site(up_id, mod_res, mod_pos)[source]¶

Find site on human ref seq corresponding to (possibly non-human) site.

Parameters:	up_id (str) – Uniprot ID of the modified protein (generally human, rat, or mouse). mod_res (str) – Modified amino acid residue. mod_pos (str) – Amino acid sequence position.
Returns:	Returns amino acid position on the human reference sequence corresponding to the site on the given protein.
Return type:	str

protmapper.phosphosite_client.sites_only(exclude_isoforms=False)[source]¶

Return PhosphositePlus data as a flat list of proteins and sites.

Parameters:	exclude_isoforms (bool) – Whether to exclude sites for protein isoforms. Default is False (includes isoforms).
Returns:	Each tuple consists of (uniprot_id, residue, position).
Return type:	list of tuples