def check_blast_status(enzyme_type):
seqs = Sequence.objects(
db.Q(enzyme_type=enzyme_type) & db.Q(bioinformatics_ignore__ne=True)
& db.Q(reviewed=True))
enz_type_obj = EnzymeType.objects(enzyme_type=enzyme_type)[0]
all_complete = True
for seq in seqs:
if seq.blast is None:
all_complete = False
enz_type_obj.bioinformatics_status = 'Queued for update'
enz_type_obj.save()
if all_complete == True:
if enz_type_obj.bioinformatics_status != 'Complete':
enz_type_obj.bioinformatics_status = 'Complete'
enz_type_obj.save()
ssn_q = SSN_record.objects(enzyme_type=enz_type_obj)
if len(ssn_q) == 1:
ssn_record = SSN_record.objects(enzyme_type=enz_type_obj)[0]
ssn_record.status = 'Queued for update'
ssn_record.save()
def remove_sequence():
user = user_datastore.get_user(current_user.id)
paper = Paper.objects(id=request.form['paper_id'])[0]
enzyme_name = request.form['enzyme_name']
seq = Sequence.objects(enzyme_name=enzyme_name)[0]
if len(
Activity.objects(
db.Q(enzyme_name=seq.enzyme_name) & db.Q(paper=paper))) != 0:
result = {
'status':
'danger',
'msg':
'Can not remove sequence - activity data still attached',
'issues': [
'Please remove references to this sequence in the activity section before removing'
]
}
return jsonify(result=result)
else:
if paper in seq.papers:
seq.papers.remove(paper)
seq.save()
if len(seq.papers) == 0 and (seq.sequence == ''
or seq.sequence is None):
seq.delete()
papers_functions.tag_paper_with_enzyme_types(paper)
result = {
'status': 'success',
'msg': 'Sequence removed from paper',
'issues': []
}
flash("Sequence removed from paper", 'success')
return jsonify(result=result)
def ssn_object():
enzyme_type = request.form['enzyme_type']
enzyme_type_obj = EnzymeType.objects(enzyme_type=enzyme_type)[0]
ssn_obj = SSN_record.objects(enzyme_type=enzyme_type_obj)[0]
num_biocatdb = Sequence.objects(enzyme_type=enzyme_type).count()
num_uniref = UniRef50.objects(enzyme_type=enzyme_type_obj).count()
precalc_choices = {}
for score in ssn_obj.num_at_alignment_score:
clusters = ssn_obj.num_at_alignment_score[score]
idt = ssn_obj.identity_at_alignment_score[score]
choice_text = f"{score}, {clusters} clusters, avg identity {idt[0]} ± {idt[1]}"
precalc_choices[score] = choice_text
result = {
'status': ssn_obj.status,
'num_biocatdb': num_biocatdb,
'num_uniref': num_uniref,
'precalculated': precalc_choices
}
return jsonify(result=result)
def leaderboard():
contributor_role = Role.objects(name='contributor')[0]
contributors = User.objects(roles=contributor_role)
papers_dict = {}
sequence_dict = {}
activity_dict = {}
for user in contributors:
username = f"{user.first_name} {user.last_name}, {user.affiliation}"
num_papers = len(Paper.objects(owner=user))
num_sequences = len(Sequence.objects(owner=user))
papers_dict[username] = num_papers
sequence_dict[username] = num_sequences
papers_dict = {k: v for k, v in sorted(papers_dict.items(), key=lambda item: item[1], reverse=True)}
papers_dict = {k: v for k, v in papers_dict.items() if v != 0}
sequence_dict = {k: v for k, v in sorted(sequence_dict.items(), key=lambda item: item[1], reverse=True)}
sequence_dict = {k: v for k, v in sequence_dict.items() if v != 0}
return render_template('leaderboard.html',
top_papers=papers_dict,
top_sequences=sequence_dict)
def delete_paper():
user = user_datastore.get_user(current_user.id)
paper = Paper.objects(id=request.form['paper_id'])[0]
if not check_permission.check_paper_permission(current_user.id, paper):
result = {
'status': 'danger',
'msg': 'You are not the owner of this paper',
'issues': ['Assign this paper to yourself in order to delete it']
}
return jsonify(result=result)
elif len(Sequence.objects(papers=paper)) != 0:
result = {
'status': 'danger',
'msg': 'Paper still contains sequences',
'issues':
['Please remove any sequences from paper before deleting']
}
return jsonify(result=result)
elif len(Activity.objects(paper=paper)) != 0:
result = {
'status':
'danger',
'msg':
'Paper still contains activity data',
'issues':
['Please remove any activity data from paper before deleting']
}
return jsonify(result=result)
else:
paper.delete()
result = {'status': 'success', 'msg': 'Paper deleted', 'issues': []}
return jsonify(result=result)
def add_new_enzymes():
enzyme_type = request.form['enzyme_type']
existing_name = request.form['existing_name']
new_name = request.form['new_name']
user = user_datastore.get_user(current_user.id)
paper = Paper.objects(id=request.form['paper_id'])[0]
if enzyme_type == '' or enzyme_type is None:
result = {
'status': 'danger',
'msg': 'Must select an enzyme type',
'issues': []
}
elif existing_name == new_name and new_name == "":
result = {
'status': 'danger',
'msg': 'Must select an enzyme or enter a new name',
'issues': []
}
elif existing_name != "" and new_name != "":
result = {
'status': 'danger',
'msg': 'Choose either an existing enzyme or enter a new name',
'issues': ["(One must be blank)"]
}
elif existing_name != "":
seq = Sequence.objects(enzyme_name=existing_name)[0]
seq.papers.append(paper)
seq.save()
result = {
'status': 'success',
'msg': 'Sequence added to paper',
'issues': []
}
elif new_name != "":
seq = Sequence(enzyme_name=new_name,
enzyme_type=enzyme_type,
added_by=user,
owner=user,
papers=[paper])
seq.save()
if user not in paper.edits_by:
paper.edits_by.append(user)
papers_functions.tag_paper_with_enzyme_types(paper)
result = {
'status': 'success',
'msg': 'Sequence added to paper',
'issues': []
}
else:
result = {
'status': 'danger',
'msg': 'Error creating new enzyme',
'issues': []
}
return jsonify(result=result)
def get_sequences_of_same_type():
enzyme_type = Sequence.objects(
enzyme_name=request.form['enzyme_name'])[0].enzyme_type
result = seqs_of_type(enzyme_type)
return jsonify(result=result)
'w') as file:
for seq in list(seqs) + list(bioinf_seqs):
name = seq.enzyme_name
seq = seq.sequence.replace('\n', '')
file.write(f'>{name}\n')
file.write(f"{seq}\n")
def log(self, msg, level=1):
if self.log_level >= level:
print(f"ABA_Blaster ({self.enzyme_type}): {msg}")
@staticmethod
def _calc_alignment_score(bitscore, query_length, subject_length):
two = Decimal(2)
bitscore = Decimal(bitscore)
x = np.power(two, -bitscore) * query_length * subject_length
alignment_score = int(-np.log10(x))
return alignment_score
if __name__ == '__main__':
from retrobiocat_web.mongo.default_connection import make_default_connection
make_default_connection()
seq_obj = Sequence.objects(enzyme_type='AAD')[0]
etb = AllByAllBlaster('AAD', log_level=1)
etb.make_blast_db()
alignment_names, alignment_scores, identities, coverages = etb.get_alignments(
seq_obj)
def _get_sequence_object(enzyme_name):
if 'UniRef50' in enzyme_name:
return UniRef50.objects(enzyme_name=enzyme_name)[0]
else:
return Sequence.objects(enzyme_name=enzyme_name)[0]
'Running Blasts')
seqs = Sequence.objects(
db.Q(enzyme_type=enzyme_type) & db.Q(bioinformatics_ignore__ne=True)
& db.Q(reviewed=True))
for seq in seqs:
if seq.sequence != '' and seq.sequence is not None and seq.blast is None:
if len(seq.sequence) > 50:
name = str(seq.enzyme_name)
current_app.blast_queue.enqueue(set_up_blast_job, name)
print(f'Queued blast for {seq.enzyme_name}')
else:
print(f'Not blasting {seq.enzyme_name}')
seq.blast = datetime.datetime.now()
else:
seq.blast = datetime.datetime.now()
seq.save()
current_app.blast_queue.enqueue(check_blast_status, enzyme_type)
if __name__ == '__main__':
from retrobiocat_web.mongo.default_connection import make_default_connection
make_default_connection()
seq = Sequence.objects(enzyme_type='AAD')[1]
protein_seq = seq.sequence
xml = BlastRunner().run(protein_seq)
BlastParser().parse(xml, seq)
def download_sequences():
sequences = Sequence.objects().as_pymongo()
df = pd.DataFrame(list(sequences))
resp = make_response(df.to_csv())
resp.headers["Content-Disposition"] = "attachment; filename=sequences.csv"
return resp
def load_sequence_data():
name = request.form['name']
if name == '':
return jsonify(result={})
seq = Sequence.objects(
enzyme_name=name).exclude('papers')[0].select_related()
sequences_same_type = Sequence.objects(
enzyme_type=seq.enzyme_type).distinct('enzyme_name')
sequences_same_type.sort()
seq_array = {}
for seq_same_type in sequences_same_type:
seq_array[seq_same_type] = seq_same_type
can_edit = False
self_assigned = False
other_user = False
if current_user.is_authenticated:
user = user_datastore.get_user(current_user.id)
if check_permission.check_seq_permissions(current_user.id, seq):
can_edit = True
if seq.owner == user:
self_assigned = True
else:
if seq.owner != '' and seq.owner is not None:
other_user = True
if seq.owner is None:
owner = ''
else:
owner = f"{seq.owner.first_name} {seq.owner.last_name}, {seq.owner.affiliation}"
other_names = ''
for i, name in enumerate(seq.other_names):
other_names += name
if (len(seq.other_names) > 1) and (i < len(seq.other_names) - 1):
other_names += ', '
other_identifiers = ''
for i, ident in enumerate(seq.other_identifiers):
other_identifiers += ident
if (len(seq.other_identifiers) >
1) and (i < len(seq.other_identifiers) - 1):
other_identifiers += ', '
enzyme_type_full = EnzymeType.objects(
enzyme_type=seq.enzyme_type)[0].full_name
if seq.n_tag is None:
seq.n_tag = ''
if seq.c_tag is None:
seq.c_tag = ''
if seq.pdb is None:
seq.pdb = ''
result = {
'enzyme_type': seq.enzyme_type,
'enzyme_name': seq.enzyme_name,
'sequence': seq.sequence,
'sequence_unavailable': seq.sequence_unavailable,
'n_tag': seq.n_tag,
'c_tag': seq.c_tag,
'accession': seq.accession,
'other_identifiers': other_identifiers,
'pdb': seq.pdb,
'mutant_of': seq.mutant_of,
'sequences': seq_array,
'notes': seq.notes,
'bioinformatics_ignore': seq.bioinformatics_ignore,
'can_edit': can_edit,
'self_assigned': self_assigned,
'owner_is_another_user': other_user,
'other_names': other_names,
'owner': owner,
'enzyme_type_full': enzyme_type_full
}
return jsonify(result=result)
def save_or_add_seqs(data_list, paper):
# Used by upload excel
user = user_datastore.get_user(current_user.id)
issues = []
enzyme_types = EnzymeType.objects().distinct('enzyme_type')
for seq_dict in data_list:
if 'sequence_unavailable' in seq_dict:
if seq_dict['sequence_unavailable'] == '':
seq_dict['sequence_unavailable'] = 'False'
if 'structure' in seq_dict:
if seq_dict['structure'] == '':
seq_dict['structure'] = 'False'
if 'sequence' in seq_dict:
seq_dict['sequence'] = seq_dict['sequence'].replace('\n', '')
seq_dict['sequence'] = seq_dict['sequence'].replace(' ', '')
if seq_dict.get('enzyme_name', '') == '':
issues.append(f"Sequence must have a name")
else:
if len(Sequence.objects(enzyme_name=seq_dict['enzyme_name'])) == 0:
if seq_dict.get('enzyme_type', '') not in enzyme_types:
print(
f"Enzyme type {seq_dict.get('enzyme_type', '')} does not exist"
)
issues.append(
f"Enzyme type {seq_dict.get('enzyme_type', '')} does not exist"
)
elif sequence_check(seq_dict.get('sequence', '')) == False:
print(
f"Amino acid sequence for {seq_dict['enzyme_name']} uses incorrect amino acid characters"
)
issues.append(
f"Amino acid sequence for {seq_dict['enzyme_name']} uses incorrect amino acid characters"
)
else:
print('Creating new sequence..')
seq = Sequence(enzyme_name=seq_dict['enzyme_name'],
enzyme_type=seq_dict['enzyme_type'],
other_names=seq_dict.get('other_names',
'').split(', '),
sequence=seq_dict.get('sequence', ''),
n_tag=seq_dict.get('n_tag', ''),
c_tag=seq_dict.get('c_tag', ''),
sequence_unavailable=strtobool(
seq_dict.get('sequence_unavailable',
'False')),
accession=seq_dict.get('accession', ''),
other_identifiers=seq_dict.get(
'other_names', '').split(', '),
pdb=seq_dict.get('pdb', ''),
mutant_of=seq_dict.get('mutant_of', ''),
notes=seq_dict.get('notes', ''),
papers=[paper],
owner=user)
seq.save()
else:
seq = Sequence.objects(enzyme_name=seq_dict['enzyme_name'])[0]
if paper not in seq.papers:
seq.papers.append(paper)
if seq.owner == user or seq.owner is None:
seq.owner = user
other_names = seq_dict.get('other_names', '').split(', ')
seq.other_names.extend(other_names)
if (seq.sequence is None or seq.sequence == ''):
seq.sequence = seq_dict.get('sequence', '')
if strtobool(seq_dict.get('sequence_unavailable',
'False')) == True:
seq.sequence_unavailable = True
if (seq.accession is None or seq.accession == ''):
seq.accession = seq_dict.get('accession', '')
if seq_dict.get('pdb', '') != '':
seq.pdb = seq_dict.get('pdb', '')
if (seq.mutant_of is None or seq.mutant_of == ''):
seq.mutant_of = seq_dict.get('mutant_of', '')
if (seq.notes is None or seq.notes == ''):
seq.notes = seq_dict.get('notes', '')
else:
print(
'Sequence already exists but owned by another user - added to paper, but no data updated'
)
issues.append(
'Sequence already exists but owned by another user - added to paper, but no data updated'
)
seq.save()
return issues
def df_to_db(spec_df):
#added_by_dict = make_added_by_user_dict()
print('Saving biocatdb_2 excel to mongodb..')
for i, row in spec_df.iterrows():
html_doi = str(row['html_doi'])
doi = str(row['html_doi'])
added_by_string = str(row['added_by'])
list_html_to_remove = [
'https://doi.org/', 'http://doi.org/', 'http://dx.doi.org/'
]
for to_remove in list_html_to_remove:
if to_remove in doi:
doi = html_doi.replace(to_remove, '')
if len(Paper.objects(doi=doi)) == 0:
paper = Paper(short_citation=str(row['short_citation']),
html=html_doi,
doi=doi)
paper = paper.save()
print(f"{row['short_citation']} added")
else:
paper = Paper.objects(doi=doi)[0]
if row['enzyme_type'] is not None and row['enzyme_type'] != '' and type(
row['enzyme_type']) == str:
if len(EnzymeType.objects(enzyme_type=row['enzyme_type'])) == 0:
enz_type = EnzymeType(enzyme_type=row['enzyme_type'],
description='')
enz_type.save()
if row['enzyme_name'] is not None and row['enzyme_name'] != '' and type(
row['enzyme_name']) == str:
if len(Sequence.objects(enzyme_name=row['enzyme_name'])) == 0:
seq = Sequence(enzyme_name=check_is_nan(row['enzyme_name']),
enzyme_type=check_is_nan(row['enzyme_type']),
papers=[paper])
seq.save()
else:
seq = Sequence.objects(enzyme_name=row['enzyme_name'])[0]
if paper not in seq.papers:
seq.papers.append(paper)
seq = seq.save()
if row['binary'] == 1:
binary = True
else:
binary = False
if row['auto_generated'] == 1:
auto_gen = True
else:
auto_gen = False
activity = Activity(
enzyme_type=check_is_nan(row['enzyme_type']),
enzyme_name=check_is_nan(row['enzyme_name']),
reaction=check_is_nan(row['reaction']),
short_citation=check_is_nan(row['short_citation']),
html_doi=check_is_nan(row['html_doi']),
added_by_string=added_by_string,
paper=paper,
cascade_num=check_is_nan(row['cascade_num']),
substrate_1_smiles=get_smile(row['substrate_1_smiles']),
substrate_2_smiles=get_smile(row['substrate_2_smiles']),
product_1_smiles=get_smile(row['product_1_smiles']),
temperature=check_is_nan(row['temperature']),
ph=check_is_nan(row['ph']),
solvent=check_is_nan(row['solvent']),
other_conditions=check_is_nan(row['other_conditions']),
notes=check_is_nan(row['notes']),
reaction_vol=check_is_nan(row['reaction_vol']),
formulation=check_is_nan(row['formulation']),
biocat_conc=check_is_nan(row['biocat_conc']),
kcat=check_is_float(row['kcat']),
km=check_is_float(row['km']),
mw=check_is_float(row['mw']),
substrate_1_conc=check_is_nan(row['substrate_1_conc']),
substrate_2_conc=check_is_nan(row['substrate_2_conc']),
specific_activity=check_is_float(row['specific_activity']),
conversion=check_is_float(row['conversion']),
conversion_time=check_is_float(row['conversion_time']),
categorical=check_is_nan(row['categorical']),
binary=binary,
selectivity=check_is_nan(row['selectivity']),
auto_generated=auto_gen)
activity.save()
print('..done')
def task_ensure_correct_sequence_naming():
seqs = Sequence.objects()
for seq in seqs:
seq.update_name(seq.enzyme_name)
def load_single_activity_data():
activity_id = request.form['activity_id']
activity = Activity.objects(id=activity_id)[0].select_related()
seq = Sequence.objects(enzyme_name=activity.enzyme_name)
sub1 = images.smitosvg_url(activity.substrate_1_smiles)
if activity.product_1_smiles == '' or activity.product_1_smiles is None:
prod = ''
else:
prod = images.smitosvg_url(activity.product_1_smiles)
if activity.substrate_2_smiles == '' or activity.substrate_2_smiles is None:
sub2 = ''
else:
sub2 = images.smitosvg_url(activity.substrate_2_smiles)
if activity.added_by is not None:
added_by = f"{activity.added_by.first_name} {activity.added_by.last_name}, {activity.added_by.affiliation}"
else:
added_by = 'Unattributed'
if activity.substrate_1_conc is None:
sub1_conc = ''
else:
sub1_conc = activity.substrate_1_conc
if sub1_conc.replace('.', '').isnumeric():
sub1_conc += ' mM'
if activity.substrate_2_conc is None:
sub2_conc = ''
else:
sub2_conc = activity.substrate_2_conc
if sub2_conc.replace('.', '').isnumeric():
sub2_conc += ' mM'
if activity.biocat_conc is None:
biocat_conc = ''
else:
biocat_conc = activity.biocat_conc
if biocat_conc.replace('.', '').isnumeric():
biocat_conc += ' mg/ml'
if activity.temperature is None:
temperature = ''
else:
temperature = activity.temperature
if temperature.replace('.', '').isnumeric():
temperature += ' <sup>o</sup>C'
if activity.ph is None:
ph = ''
else:
ph = activity.ph
if ph.replace('.', '').isnumeric():
ph = 'pH ' + ph
if activity.reaction_vol is None:
volume = ''
else:
volume = activity.reaction_vol
if volume.replace('.', '').isnumeric():
volume += ' mL scale'
if activity.binary == True:
active = 'Active'
else:
active = 'Not active'
if activity.specific_activity is None:
sa = ''
else:
sa = str(round(activity.specific_activity, 2))
sa += ' μmol / min / mg'
if activity.conversion is None:
conv = ''
else:
conv = str(int(activity.conversion)) + " % conversion"
if activity.conversion_time is not None:
conv += f" in {str(int(activity.conversion_time))} hours"
if activity.kcat is None:
kinetics = ''
else:
kinetics = f"kcat: {str(round(activity.kcat,2))} min<sup>-1</sup> km: {str(round(activity.km,2))} mM"
result = {
'short_cit': activity.paper.short_citation,
'enzyme_name': activity.enzyme_name,
'enzyme_type': activity.enzyme_type,
'reaction': activity.reaction,
'sub1_img': sub1,
'sub2_img': sub2,
'prod_img': prod,
'added_by': added_by,
'sub1_conc': sub1_conc,
'sub2_conc': sub2_conc,
'biocat_conc': biocat_conc,
'formulation': activity.formulation,
'selectivity': activity.selectivity,
'temperature': temperature,
'ph': ph,
'solvent': activity.solvent,
'volume': volume,
'other_conditions': activity.other_conditions,
'notes': activity.notes,
'active': active,
'category': activity.categorical,
'sa': sa,
'conv': conv,
'kinetics': kinetics
}
for key in result:
if result[key] is None:
result[key] = ''
return jsonify(result=result)
def save_edited_sequence():
original_name = request.form['original_name']
enzyme_name = request.form['enzyme_name']
enzyme_type = request.form['enzyme_type']
sequence = request.form['sequence']
sequence_unavailable = bool(strtobool(
request.form['sequence_unavailable']))
n_tag = request.form['n_tag']
c_tag = request.form['c_tag']
accession = request.form['accession']
other_identifiers = request.form['other_identifiers']
pdb = request.form['pdb']
mutant_of = request.form['mutant_of']
notes = request.form['notes']
other_names = request.form['other_names']
bioinformatics_ignore = bool(
strtobool(request.form['bioinformatics_ignore']))
status = 'success'
msg = 'Sequence edited'
issues = []
seq = Sequence.objects(enzyme_name=original_name)[0]
user = user_datastore.get_user(current_user.id)
if not check_permission.check_seq_permissions(current_user.id, seq):
issues.append('User does not have access to edit this sequence')
if original_name != enzyme_name:
success, msg = seq.update_name(enzyme_name)
if success is False:
issues.append(msg)
if seq.enzyme_type != enzyme_type:
success, msg = seq.update_type(enzyme_type)
if success is False:
issues.append(msg)
if seq.sequence != sequence:
success, msg = seq.update_sequence(sequence)
if success is False:
issues.append(msg)
seq.sequence_unavailable = sequence_unavailable
seq.n_tag = n_tag
seq.c_tag = c_tag
seq.accession = accession
seq.other_identifiers = other_identifiers.split(', ')
seq.pdb = pdb
seq.notes = notes
seq.mutant_of = mutant_of
seq.other_names = other_names.split(', ')
seq.bioinformatics_ignore = bioinformatics_ignore
seq.save()
self_assigned = bool(strtobool(request.form['self_assigned']))
if self_assigned == True:
seq.owner = user
elif self_assigned == False and seq.owner == user:
seq.owner = None
update_seq_papers_status(seq.enzyme_name)
if len(issues) != 0:
status = 'danger'
msg = 'Issues updating sequence'
result = {'status': status, 'msg': msg, 'issues': issues}
return jsonify(result=result)
def inject_login_mode():
inject_dict = {}
inject_dict['login_mode'] = app.config['USE_EMAIL_CONFIRMATION']
if current_user.is_authenticated:
user = User.objects(id=current_user.id).select_related()[0]
if user.has_role('enzyme_teams') and user.enzyme_teams is not None:
inject_dict['enzyme_teams'] = [
enz_type_obj.enzyme_type
for enz_type_obj in user.enzyme_teams
]
if user.has_role(
'enzyme_champion') and user.enzyme_champion is not None:
inject_dict['enzyme_champion'] = [
enz_type_obj.enzyme_type
for enz_type_obj in user.enzyme_champion
]
if user.has_role('contributor'):
inject_dict['user_papers_need_data'] = len(
Paper.objects(
Q(owner=user)
& (Q(status='Data required')
| Q(status='Enzymes need protein sequences')
| Q(status='Issues need to be resolved'))))
inject_dict['user_seqs_need_data'] = len(
Sequence.objects(
Q(owner=user)
& ((Q(sequence=None) | Q(sequence=''))
& (Q(sequence_unavailable__ne=True)))))
inject_dict['total_team_notifications'] = 0
inject_dict['team_notifications'] = {}
inject_dict['champ_seq_notifications'] = {}
inject_dict['champ_notifications'] = {}
if 'enzyme_teams' in inject_dict:
for enz_type in inject_dict['enzyme_teams']:
num_papers = len(
Paper.objects(
Q(tags=enz_type) & Q(owner=None)
& (Q(status='Data required')
| Q(status='Enzymes need protein sequences'))))
inject_dict['team_notifications'][enz_type] = num_papers
inject_dict['total_team_notifications'] += num_papers
if 'enzyme_champion' in inject_dict:
for enz_type in inject_dict['enzyme_champion']:
num_papers = len(
Paper.objects(
Q(tags=enz_type)
& Q(status='Complete - Awaiting review')))
num_seqs = len(
Sequence.objects(
Q(enzyme_type=enz_type)
& ((Q(sequence=None) | Q(sequence=''))
& (Q(sequence_unavailable__ne=True)))))
inject_dict['champ_notifications'][enz_type] = num_papers
inject_dict['champ_seq_notifications'][enz_type] = num_seqs
inject_dict[
'total_team_notifications'] += num_papers + num_seqs
return inject_dict
def set_choices(self):
self.enzyme_type.choices = [(c, c) for c in ['All'] + (list(Sequence.objects().distinct('enzyme_type')))]
self.enzyme_name.choices = [(c, c) for c in ['All'] + (list(Sequence.objects().distinct('enzyme_name')))]
sequences = Sequence.objects(
db.Q(sequence__ne=None) & db.Q(sequence__ne='')
& db.Q(enzyme_type=enzyme_type))
unirefs = UniRef90.objects(enzyme_type=enz_type_obj)
nodes = []
for seq_obj in list(unirefs) + list(sequences):
nodes.append(new_node(seq_obj))
edges = []
for ali_obj in alignments:
if ali_obj.identity >= identity and ali_obj.proteins[
0].enzyme_name != ali_obj.proteins[1].enzyme_name:
edges.append(new_edge(ali_obj))
return nodes, edges
if __name__ == '__main__':
from retrobiocat_web.mongo.default_connection import make_default_connection
make_default_connection()
enzyme_type = 'AAD'
sequences = Sequence.objects(
db.Q(sequence__ne=None) & db.Q(sequence__ne='')
& db.Q(enzyme_type=enzyme_type))
for seq in sequences:
print(seq.enzyme_name)
print(f"Sequence = '{seq.sequence}'")
def filter_papers_by_enzyme_name(papers, enzyme_name):
seqs = Sequence.objects(enzyme_name=enzyme_name).select_related()
seq_papers = [paper for paper in [seq.papers for seq in seqs]][0]
filtered_papers = [paper for paper in papers if paper in seq_papers]
return filtered_papers