def bioitem_relation_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_chemical = dict([(x.unique_key(), x) for x in nex_session.query(Chemical).all()])
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for bud_obj in bud_session.query(CVTermRel).options(joinedload('child'), joinedload('parent')).all():
parent_key = (create_format_name(bud_obj.parent.name)[:95], 'CHEMICAL')
child_key = (create_format_name(bud_obj.child.name)[:95], 'CHEMICAL')
if parent_key in key_to_chemical and child_key in key_to_chemical:
yield {'source': key_to_source['SGD'],
'relation_type': bud_obj.relationship_type,
'parent_id': key_to_chemical[parent_key].id,
'child_id': key_to_chemical[child_key].id,
'date_created': bud_obj.date_created,
'created_by': bud_obj.created_by}
bud_session.close()
nex_session.close()
def experiment_relation_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_experiment = dict([(x.unique_key(), x) for x in nex_session.query(Experiment).all()])
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for old_cv_term in bud_session.query(CVTerm).filter(CVTerm.cv_no==7).options(joinedload('parent_rels'), joinedload('parent_rels.parent')).all():
child_key = create_format_name(old_cv_term.name)
for parent_rel in old_cv_term.parent_rels:
parent_key = create_format_name(parent_rel.parent.name)
if parent_key in key_to_experiment and child_key in key_to_experiment:
yield {'source': key_to_source['SGD'],
'parent_id': key_to_experiment[parent_key].id,
'child_id': key_to_experiment[child_key].id,
'date_created': parent_rel.date_created,
'created_by': parent_rel.created_by}
else:
print 'Experiment does not exist: ' + str(parent_key) + ' ' + str(child_key)
bud_session.close()
nex_session.close()
def bioitem_tag_starter():
nex_session = nex_session_maker()
key_to_dataset = dict([(x.unique_key(), x) for x in nex_session.query(Dataset).all()])
key_to_tag = dict([(x.unique_key(), x) for x in nex_session.query(Tag).all()])
for row in make_file_starter('src/sgd/convert/data/microarray_05_14/SPELL-tags.txt')():
dataset_key = (row[1].strip()[:-4], 'DATASET')
tags = row[2].strip()
for t in [x.strip() for x in tags.split('|')]:
if t != '':
yield {
'bioitem': key_to_dataset[dataset_key],
'tag': key_to_tag[create_format_name(t)]
}
nex_session.close()
def experiment_alias_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_experiment = dict([(x.unique_key(), x) for x in nex_session.query(Experiment).all()])
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for old_cv_term in bud_session.query(CVTerm).filter(CVTerm.cv_no==7).options(joinedload('cv_dbxrefs'), joinedload('cv_dbxrefs.dbxref')).all():
experiment_key = create_format_name(old_cv_term.name)
if experiment_key in key_to_experiment:
for dbxref in old_cv_term.dbxrefs:
yield {'display_name': dbxref.dbxref_id,
'source': key_to_source['SGD'],
'category': 'APOID',
'experiment_id': key_to_experiment[experiment_key].id,
'date_created': dbxref.date_created,
'created_by': dbxref.created_by}
else:
print 'Experiment does not exist: ' + str(experiment_key)
yield None
bud_session.close()
nex_session.close()
def orphan_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for bud_obj in bud_session.query(ExperimentProperty).filter(ExperimentProperty.type == 'Reporter').all():
if bud_obj.type == 'Reporter':
yield {'display_name': bud_obj.value,
'source': key_to_source['SGD']}
for bud_obj in bud_session.query(GorefDbxref).all():
dbxref = bud_obj.dbxref
dbxref_type = dbxref.dbxref_type
if dbxref_type != 'GOID' and dbxref_type != 'EC number' and dbxref_type != 'DBID Primary' and dbxref_type != 'PANTHER' and dbxref_type != 'Prosite':
source_key = create_format_name(dbxref.source)
source = None if source_key not in key_to_source else key_to_source[source_key]
if source is None:
print 'Source not found: ' + str(source_key)
yield None
link = None
bioitem_type = None
if dbxref_type == 'UniProt/Swiss-Prot ID':
urls = dbxref.urls
if len(urls) == 1:
link = urls[0].url.replace('_SUBSTITUTE_THIS_', dbxref.dbxref_id)
bioitem_type = 'UniProtKB'
elif dbxref_type == 'UniProtKB Subcellular Location':
link = "http://www.uniprot.org/locations/" + dbxref.dbxref_id
bioitem_type = 'UniProtKB-SubCell'
elif dbxref_type == 'InterPro':
link = "http://www.ebi.ac.uk/interpro/entry/" + dbxref.dbxref_id
bioitem_type = 'InterPro'
elif dbxref_type == 'DNA accession ID':
link = None
bioitem_type = 'EMBL'
elif dbxref_type == 'Gene ID':
link = None
bioitem_type = dbxref.source
elif dbxref_type == 'HAMAP ID' or dbxref_type == 'HAMAP':
link = None
bioitem_type = 'HAMAP'
elif dbxref_type == 'PDB identifier':
link = None
bioitem_type = 'PDB'
elif dbxref_type == 'Protein version ID':
link = None
bioitem_type = 'protein_id'
elif dbxref_type == 'UniPathway ID':
link = 'http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=' + dbxref.dbxref_id
bioitem_type = 'UniPathway'
elif dbxref_type == 'UniProtKB Keyword':
link = 'http://www.uniprot.org/keywords/' + dbxref.dbxref_id
bioitem_type = 'UniProtKB-KW'
yield {'display_name': dbxref.dbxref_id,
'link': link,
'source': source,
'description': dbxref.dbxref_name,
'bioitem_type': bioitem_type}
bud_session.close()
nex_session.close()
def domain_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
panther_id_to_description = {}
for row in make_file_starter('src/sgd/convert/data/PANTHER9.0_HMM_classifications.txt')():
panther_id_to_description[row[0]] = row[1].lower()
for row in make_file_starter('src/sgd/convert/data/domains.tab')():
source_key = row[3].strip()
if source_key.startswith('ProSite'):
source_key = 'Prosite'
if source_key.startswith('SignalP'):
source_key = 'SignalP'
if source_key.startswith('Hamap'):
source_key = 'HAMAP'
if source_key == 'Coils':
source_key = '-'
display_name = row[4].strip()
description = row[5].strip()
interpro_id = None
interpro_description = None
if len(row) == 13:
interpro_id = row[11].strip()
interpro_description = row[12].strip()
source_key = create_format_name(source_key)
source = None if source_key not in key_to_source else key_to_source[source_key]
description = None if description == '' else description
interpro_description = None if interpro_description == '' else interpro_description
interpro_id = None if interpro_id == '' else interpro_id
if source_key == 'PANTHER':
if display_name in panther_id_to_description:
yield {'display_name': display_name,
'source': source,
'description': panther_id_to_description[display_name],
'bioitem_type': source_key,
'interpro_id': interpro_id,
'interpro_description': interpro_description}
elif source_key is not None:
yield {'display_name': display_name,
'source': source,
'description': description if description is not None else interpro_description,
'bioitem_type': source_key,
'interpro_id': interpro_id,
'interpro_description': interpro_description}
else:
print 'Source not found: ' + source_key
for row in make_file_starter('src/sgd/convert/data/TF_family_class_accession04302013.txt')():
description = 'Class: ' + row[4] + ', Family: ' + row[3]
yield {'display_name': row[0],
'source': key_to_source['JASPAR'],
'description': description,
'bioitem_type': 'JASPAR'}
yield {'display_name': 'predicted signal peptide',
'source': key_to_source['SignalP'],
'description': 'predicted signal peptide',
'bioitem_type': 'SignalP'}
yield {'display_name': 'predicted transmembrane domain',
'source': key_to_source['TMHMM'],
'description': 'predicted transmembrane domain',
'bioitem_type': 'TMHMM'}
for bud_obj in bud_session.query(Dbxref).filter(or_(Dbxref.dbxref_type == 'PANTHER', Dbxref.dbxref_type == 'Prosite')).all():
dbxref_type = bud_obj.dbxref_type
source_key = create_format_name(bud_obj.source)
source = None if source_key not in key_to_source else key_to_source[source_key]
if source is None:
print source_key
yield None
bioitem_type = None
if dbxref_type == 'Prosite ID':
bioitem_type = 'Prosite'
elif dbxref_type == 'PANTHER':
bioitem_type = 'PANTHER'
if bioitem_type == 'PANTHER':
if display_name in panther_id_to_description:
yield {'display_name': bud_obj.dbxref_id,
'source': source,
'description': panther_id_to_description[bud_obj.dbxref_id],
'bioitem_type': bioitem_type}
else:
yield {'display_name': bud_obj.dbxref_id,
'source': source,
'description': bud_obj.dbxref_name,
'bioitem_type': bioitem_type}
bud_session.close()
nex_session.close()
def experiment_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for bud_obj in make_obo_file_starter('src/sgd/convert/data/eco.obo')():
description = None if 'def' not in bud_obj else bud_obj['def']
if description is not None and description.find('[') >= 0:
description = description[:description.find('[')-1]
if description is not None and description.find('"') >= 0:
description = description[1:-1]
yield {'display_name': bud_obj['name'],
'source': key_to_source['ECO'],
'description': description,
'eco_id': bud_obj['id']}
for bud_obj in bud_session.query(CVTerm).filter(CVTerm.cv_no==7).all():
format_name = create_format_name(bud_obj.name)
yield {'display_name': bud_obj.name,
'source': key_to_source['SGD'],
'description': bud_obj.definition,
'category': 'large-scale survey' if format_name in large_scale_survey else 'classical genetics' if format_name in classical_genetics else None,
'date_created': bud_obj.date_created,
'created_by': bud_obj.created_by}
for row in make_file_starter('src/sgd/convert/data/2014-05-15_reg_data/Venters_Macisaac_Hu05-12-2014_regulator_lines')():
source_key = row[11].strip()
if source_key in key_to_source:
yield {'display_name': row[4] if row[4] != '' else row[5],
'source': None if source_key not in key_to_source else key_to_source[source_key],
'eco_id': row[5]}
else:
print 'Source not found: ' + str(source_key)
for row in make_file_starter('src/sgd/convert/data/2014-05-15_reg_data/SGD_data_05_14_2014')():
source_key = row[11].strip()
if source_key in key_to_source:
yield {'display_name': row[4] if row[4] != '' else row[5],
'source': None if source_key not in key_to_source else key_to_source[source_key],
'eco_id': row[5]}
else:
print 'Source not found: ' + str(source_key)
for row in make_file_starter('src/sgd/convert/data/2014-05-15_reg_data/Madhani_fixed')():
if len(row) >= 10:
if source_key in key_to_source:
source_key = row[11].strip()
yield {'display_name': row[5] if row[5] != '' else row[4],
'source': None if source_key not in key_to_source else key_to_source[source_key],
'eco_id': row[4]}
else:
print 'Source not found: ' + str(source_key)
for row in make_file_starter('src/sgd/convert/data/2014-05-15_reg_data/Pimentel_PMID22616008.txt')():
if len(row) >= 10:
if source_key in key_to_source:
source_key = row[11].strip()
yield {'display_name': row[4] if row[4] != '' else row[5],
'source': None if source_key not in key_to_source else key_to_source[source_key],
'eco_id': row[5]}
else:
print 'Source not found: ' + str(source_key)
for row in make_file_starter('src/sgd/convert/data/yetfasco_data.txt', delimeter=';')():
expert_confidence = row[8][1:-1]
if expert_confidence == 'High':
yield {'display_name': row[9][1:-1],
'source': key_to_source['YeTFaSCo']}
yield {'display_name': 'protein abundance', 'source': key_to_source['SGD']}
yield {'display_name': 'EXP', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/exp-inferred-experiment', 'description': 'Inferred from Experiment'}
yield {'display_name': 'IDA', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ida-inferred-direct-assay', 'description': 'Inferred from Direct Assay'}
yield {'display_name': 'IPI', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ipi-inferred-physical-interaction', 'description': 'Inferred from Physical Interaction'}
yield {'display_name': 'IMP', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/imp-inferred-mutant-phenotype', 'description': 'Inferred from Mutant Phenotype'}
yield {'display_name': 'IGI', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/igi-inferred-genetic-interaction', 'description': 'Inferred from Genetic Interaction'}
yield {'display_name': 'IEP', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/iep-inferred-expression-pattern', 'description': 'Inferred from Expression Pattern'}
yield {'display_name': 'ISS', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/iss-inferred-sequence-or-structural-similarity', 'description': 'Inferred from Sequence or Structural Similarity'}
yield {'display_name': 'ISA', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/isa-inferred-sequence-alignment', 'description': 'Inferred from Sequence Alignment'}
yield {'display_name': 'ISO', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/iso-inferred-sequence-orthology', 'description': 'Inferred from Sequence Orthology'}
yield {'display_name': 'ISM', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ism-inferred-sequence-model', 'description': 'Inferred from Sequence Model'}
yield {'display_name': 'IGC', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/igc-inferred-genomic-context', 'description': 'Inferred from Genomic Context'}
yield {'display_name': 'IBA', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/iba-inferred-biological-aspect-ancestor', 'description': 'Inferred from Biological aspect of Ancestor'}
yield {'display_name': 'IBD', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ibd-inferred-biological-aspect-descendent', 'description': 'Inferred from Biological aspect of Descendent'}
yield {'display_name': 'IKR', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ikr-inferred-key-residues', 'description': 'Inferred from Key Residues'}
yield {'display_name': 'IRD', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ird-inferred-rapid-divergence', 'description': 'Inferred from Rapid Divergence'}
yield {'display_name': 'RCA', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/rca-inferred-reviewed-computational-analysis', 'description': 'inferred from Reviewed Computational Analysis'}
yield {'display_name': 'TAS', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/tas-traceable-author-statement', 'description': 'Traceable Author Statement'}
yield {'display_name': 'NAS', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/nas-non-traceable-author-statement', 'description': 'Non-traceable Author Statement'}
yield {'display_name': 'IC', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/ic-inferred-curator', 'description': 'Inferred by Curator'}
yield {'display_name': 'ND', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/nd-no-biological-data-available', 'description': 'No Biological Data Available'}
yield {'display_name': 'IEA', 'source': key_to_source['GO'], 'link': 'http://www.geneontology.org/page/automatically-assigned-evidence-codes', 'description': 'Inferred from Electronic Annotation'}
bud_session.close()
nex_session.close()
def orphan_starter():
bud_session = bud_session_maker()
nex_session = nex_session_maker()
key_to_source = dict([(x.unique_key(), x) for x in nex_session.query(Source).all()])
for bud_obj in bud_session.query(ExperimentProperty).filter(ExperimentProperty.type == 'Reporter').all():
if bud_obj.type == 'Reporter':
yield {'display_name': bud_obj.value,
'source': key_to_source['SGD']}
f = open('src/sgd/convert/data/gp_association.559292_sgd')
soid = None
for line in f:
pieces = line.split('\t')
if len(pieces) < 11:
continue
go_extensions = pieces[10]
if go_extensions == '' or '(SO:' not in go_extensions:
continue
items = go_extensions.replace(',', '|').split('|')
for item in items:
if "(SO:" not in item:
continue
soid = item.split('(')[1][:-1]
yield { 'display_name': soid,
'source': key_to_source['SGD'],
'bioitem_type': 'SO' }
f.close()
for bud_obj in bud_session.query(GorefDbxref).all():
dbxref = bud_obj.dbxref
dbxref_type = dbxref.dbxref_type
if dbxref_type != 'GOID' and dbxref_type != 'EC number' and dbxref_type != 'DBID Primary' and dbxref_type != 'PANTHER' and dbxref_type != 'Prosite':
source_key = create_format_name(dbxref.source)
source = None if source_key not in key_to_source else key_to_source[source_key]
if source is None:
print 'Source not found: ' + str(source_key)
yield None
link = None
bioitem_type = None
if dbxref_type == 'UniProt/Swiss-Prot ID':
urls = dbxref.urls
if len(urls) == 1:
link = urls[0].url.replace('_SUBSTITUTE_THIS_', dbxref.dbxref_id)
bioitem_type = 'UniProtKB'
elif dbxref_type == 'UniProtKB Subcellular Location':
link = "http://www.uniprot.org/locations/" + dbxref.dbxref_id
bioitem_type = 'UniProtKB-SubCell'
elif dbxref_type == 'InterPro':
link = "http://www.ebi.ac.uk/interpro/entry/" + dbxref.dbxref_id
bioitem_type = 'InterPro'
elif dbxref_type == 'DNA accession ID':
link = None
bioitem_type = 'EMBL'
elif dbxref_type == 'Gene ID':
link = None
bioitem_type = dbxref.source
elif dbxref_type == 'HAMAP ID' or dbxref_type == 'HAMAP':
link = None
bioitem_type = 'HAMAP'
elif dbxref_type == 'PDB identifier':
link = None
bioitem_type = 'PDB'
elif dbxref_type == 'Protein version ID':
link = None
bioitem_type = 'protein_id'
elif dbxref_type == 'UniPathway ID':
link = 'http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=' + dbxref.dbxref_id
bioitem_type = 'UniPathway'
elif dbxref_type == 'UniProtKB Keyword':
link = 'http://www.uniprot.org/keywords/' + dbxref.dbxref_id
bioitem_type = 'UniProtKB-KW'
yield {'display_name': dbxref.dbxref_id,
'link': link,
'source': source,
'description': dbxref.dbxref_name,
'bioitem_type': bioitem_type}
bud_session.close()
nex_session.close()