def search(args):
"""Uses PhosPhAt API to return computationally predicted phosphorylation
hotspots when given an AGI code.
Args:
All arguments are stored in a single dict.
transcript_id: AGI Transcript Identifier. Refers to a specific protein.
Example value: 'AT1G06410.1'
"""
# tools.validate_args is a custom method that validates the transcript ID.
# It will throw an exception if the ID is invalid.
tools.validate_args(args)
# tools.request_data is a custom method in the services.common.tools module.
# It contacts the remote host PhosPhAt and returns phosphorylation data
# as a dict, which is then stored in phos_sites.
# This method will raise an exception if it can't connect to PhosPhAt.
hotspots = tools.request_data(args['transcript_id'], API_METHOD)
# phos_sites is a dict, and phos_sites['result'] is a dict within phos_sites.
for h in hotspots['result']:
# h refers to each dict within hotspots['result'].
extracted_data = {}
extracted_data['hotspot_sequence'] = h['hsp_hotspot_sequenz']
extracted_data['start_position'] = h['hsp_hotspot_start']
extracted_data['end_position'] = h['hsp_hotspot_stop']
# Adama requires JSON objects be printed and separated by three dashes
print json.dumps(extracted_data) + '\n---'
def search(args):
"""Uses PhosPhAt API to get predicted phosphorylation sites.
Args:
All arguments are stored in a single dict.
transcript_id: AGI Transcript Identifier. Refers to a specific protein.
Example value: 'AT1G06410.1'
"""
# tools.validate_args is a custom method that validates the transcript ID.
# It will throw an exception if the ID is invalid.
tools.validate_args(args)
# tools.request_data is a custom method in the services.common.tools module.
# It contacts the remote host PhosPhAt and returns phosphorylation data
# as a dict, which is then stored in phos_sites.
# This method will raise an exception if it can't connect to PhosPhAt.
phos_sites = tools.request_data(args['transcript_id'], API_METHOD)
# phos_sites is a dict, and phos_sites['result'] is a dict within phos_sites.
for p_site in phos_sites['result']:
# Each p_site is a dict within phos_sites['result'].
extracted_data = {}
extracted_data['position_in_protein'] = p['prd_position']
extracted_data['prediction_score'] = p['prd_score']
extracted_data['thirteen_mer_sequence'] = p['prd_13mer']
# Adama requires JSON objects be printed and separated by three dashes
print json.dumps(extracted_data) + '\n---'
def search(args):
"""Uses PhosPhAt API to get predicted phosphorylation sites.
Args:
All arguments are stored in a single dict.
transcript_id: AGI Transcript Identifier. Refers to a specific protein.
Example value: 'AT1G06410.1'
"""
# tools.validate_args is a custom method that validates the transcript ID.
# It will throw an exception if the ID is invalid.
tools.validate_args(args)
# tools.request_data is a custom method in the services.common.tools module.
# It contacts the remote host PhosPhAt and returns phosphorylation data
# as a dict, which is then stored in phos_sites.
# This method will raise an exception if it can't connect to PhosPhAt.
phos_sites = tools.request_data(args['transcript_id'], API_METHOD)
# phos_sites is a dict, and phos_sites['result'] is a dict within phos_sites.
for p_site in phos_sites['result']:
# Each p_site is a dict within phos_sites['result'].
extracted_data = {}
extracted_data['position_in_protein'] = p['prd_position']
extracted_data['prediction_score'] = p['prd_score']
extracted_data['thirteen_mer_sequence'] = p['prd_13mer']
# Adama requires JSON objects be printed and separated by three dashes
print json.dumps(extracted_data) + '\n---'
def search(args):
"""Uses PhosPhAt API to return experimentally determined phosphorylation
hotspots when given an AGI code.
Args:
All arguments are stored in a single dict.
transcript_id: AGI Transcript Identifier. Refers to a specific protein.
Example value: 'AT1G01540.1'
"""
# tools.validate_args is a custom method that validates the transcript ID.
# It will throw an exception if the ID is invalid.
tools.validate_args(args)
# tools.request_data is a custom method in the services.common.tools module.
# It contacts the remote host PhosPhAt and returns phosphorylation data
# as a dict, which is then stored in phos_sites.
# This method will raise an exception if it can't connect to PhosPhAt.
hotspots = tools.request_data(args['transcript_id'], API_METHOD)
# phos_sites is a dict, and phos_sites['result'] is a dict within phos_sites.
for h in hotspots['result']:
# h refers to each dict within hotspots['result'].
extracted_data = {}
extracted_data['hotspot_sequence'] = h['hspExp_hotspot_sequenz']
extracted_data['start_position'] = h['hspExp_hotspot_start']
extracted_data['end_position'] = h['hspExp_hotspot_stop']
# Adama requires JSON objects be printed and separated by three dashes
print json.dumps(extracted_data) + '\n---'
def search(args):
"""Uses PhosPhAt API to return detailed experimental phosphorylation sites
given a modified peptide sequence.
Args:
All arguments are stored in a single dict (args).
transcript_id: AGI Transcript Identifier. Refers to a specific protein.
Example value: 'AT1G06410.1'
"""
# tools.validate_args is a custom method that validates the transcript ID.
# It will throw an exception if the ID is invalid.
tools.validate_args(args)
# tools.request_data is a custom method in the services.common.tools module.
# It contacts the remote host PhosPhAt and returns phosphorylation data
# as a dict, which is then stored in phos_sites.
# This method will raise an exception if it can't connect to PhosPhAt.
phos_sites = tools.request_data(args['transcript_id'], API_METHOD)
# phos_sites is a dict, and phos_sites['result'] is a dict within phos_sites.
for p_site in phos_sites['result']:
# Each p_site is a dict within phos_sites['result'].
extracted_data = {}
extracted_data['peptide_sequence'] = p_site['pep_sequence']
extracted_data['modified_sequence'] = p_site['modifiedsequence']
extracted_data['protein_sequence'] = p_site['prot_sequence']
# PhosPhAt is in Germany and uses commas instead of decimal points
extracted_data['mass'] = p_site['mass'].replace(",", ".")
extracted_data['position_in_peptide'] = p_site['position']
extracted_data['modification_code'] = p_site['modificationType']
# Call tools.expand_mod_type to make returned data more comprehensible
extracted_data['modification_type'] = tools.expand_mod_type(
p_site['modificationType'])
# Adama requires JSON objects be printed and separated by three dashes
print json.dumps(extracted_data) + '\n---'