PTM

CoDIAC.PTM.write_PTM_features(Interpro_ID, uniprot_ref_file, feature_dir, mapping_file='', n_term_offset=0, c_term_offset=0, gap_threshold=0.7, num_PTM_threshold=5, PHOSPHOSITE_PLUS=False)

Writes all PTM features from ProteomeScout or PhosphoSitePlus on Interpro domains from a uniprot reference file, if there are more than num_PTM_threshold that occur across all domains of that type in the reference. Returns the ptm_count_dict for reference and the feature dict that is generated to write the files. Files are named Interpro_ID_<PTM_Type>.feature and the reference fasta is also generated so that it is clear the features are attached to that particular run of the domains.

Parameters:

Interpro_ID: string

Interpro ID - for example in a reference line such as SH3_domain:IPR001452:82:143; SH2:IPR000980:147:246; Prot_kinase_dom:IPR000719:271:524 the interpro ID for the SH3_domain is IPR001452; for the SH2 domain is IPR000980

uniprot_reference_file: string

File location that contains the reference of interest (like produced from Uniprot.makeRefFile)

feature_dir: string

Feature Directory to place files in

mapping_file: string

A CSV file location, if wanted, that holds a translation of the long header into a shorter header If this is an empty string, then it will not attempt mapping

n_term_offset: int

Number of amino acids to extend in the n-term direction (up to start of protein)

c_term_offset: int

Number of amino acids to extend in the c-term direction (up to end of protein)

gap_threshold: float

fraction gap allowed before dispanding with PTM translation from ProteomeScout

num_PTM_threshold: int

Number of PTMs in all domains of a type required to generate a feature file

PHOSPHOSITE_PLUS: bool

If True, will generate PTMs from PhosphoSitePlus instead of ProteomeScout. See PhosphoSitePlus_Tools.py convert_pSiteDataFiles can be used to update or create the API-formatted files. These resources are stored in GitHub LFS.

Returns:

file_list: list

List of files generated as features

ptm_count_dict: dict

keys are the modification type and values are total number encountered

domain_feature_dict: dict of dicts

keys are the fasta headers Inner dict keys are the modification types and the values of this is a list of zero-based positions.