def aligned_sites(self):
"""Aligns all binding sites using LASAGNA."""
site_instances = [
meta_site.delegate.site_instance for meta_site in self.meta_sites
if meta_site.site_type == 'motif_associated'
]
return lasagna.lasagna(site_instances)
def site_entry_get_form(wiz, form):
"""Construct the form for site entry step."""
c = session_utils.get(wiz.request.session, 'previously_curated_paper')
# if paper is previously curated, prepopulate fields
if c:
# Delete session data, if user change any field and then come back,
# Store users last entered data, instead of populated data.
session_utils.remove(wiz.request.session, 'previously_curated_paper')
# populate motifs for the curator to map sites to one of them.
genomes = session_utils.get(wiz.request.session, 'genomes')
TF_instances = session_utils.get(wiz.request.session, 'TF_instances')
csis = models.Curation_SiteInstance.objects.filter(
site_type='motif_associated',
site_instance__genome__in=genomes,
curation__TF_instances__in=TF_instances)
# Add motifs as site_type choices
site_type_choices = []
motif_ids = csis.values_list('motif_id', flat=True).distinct()
for motif_id in motif_ids:
sites = [csi.site_instance
for csi in csis.filter(motif_id=motif_id)]
weblogo = mark_safe("<img src='%s'" %
bioutils.weblogo_uri(lasagna.lasagna(sites)))
site_type_choices.append((motif_id, weblogo))
# Add non-motif-associated and variable-motif-associated
site_type_choices.append((max(motif_ids)+1 if motif_ids else 0,
'motif-associated (new motif)'))
site_type_choices.append(('var_motif_associated',
'variable motif associated'))
site_type_choices.append(('non_motif_associated',
'non-motif associated'))
form.fields['site_type'].choices = site_type_choices
# if not high-throughput mode, delete related fields
if not session_utils.get(wiz.request.session, 'high_throughput_curation'):
del form.fields['peaks']
del form.fields['assay_conditions']
del form.fields['method_notes']
del form.fields['peak_techniques']
else: # high-throughput mode
# Populate peak techniques
techniques = session_utils.get(wiz.request.session, 'techniques')
choices = [(t.technique_id, t.name) for t in techniques]
form.fields['peak_techniques'].choices = choices
return form
def site_entry_get_form(wiz, form):
"""Construct the form for site entry step."""
c = session_utils.get(wiz.request.session, 'previously_curated_paper')
# if paper is previously curated, prepopulate fields
if c:
# Delete session data, if user change any field and then come back,
# Store users last entered data, instead of populated data.
session_utils.remove(wiz.request.session, 'previously_curated_paper')
# populate motifs for the curator to map sites to one of them.
genomes = session_utils.get(wiz.request.session, 'genomes')
TF_instances = session_utils.get(wiz.request.session, 'TF_instances')
csis = models.Curation_SiteInstance.objects.filter(
site_type='motif_associated',
site_instance__genome__in=genomes,
curation__TF_instances__in=TF_instances)
# Add motifs as site_type choices
site_type_choices = []
motif_ids = csis.values_list('motif_id', flat=True).distinct()
for motif_id in motif_ids:
sites = [csi.site_instance for csi in csis.filter(motif_id=motif_id)]
weblogo = mark_safe("<img src='%s'" %
bioutils.weblogo_uri(lasagna.lasagna(sites)))
site_type_choices.append((motif_id, weblogo))
# Add non-motif-associated and variable-motif-associated
site_type_choices.append((max(motif_ids) + 1 if motif_ids else 0,
'motif-associated (new motif)'))
site_type_choices.append(
('var_motif_associated', 'variable motif associated'))
site_type_choices.append(('non_motif_associated', 'non-motif associated'))
form.fields['site_type'].choices = site_type_choices
# if not high-throughput mode, delete related fields
if not session_utils.get(wiz.request.session, 'high_throughput_curation'):
del form.fields['peaks']
del form.fields['assay_conditions']
del form.fields['method_notes']
del form.fields['peak_techniques']
else: # high-throughput mode
# Populate peak techniques
techniques = session_utils.get(wiz.request.session, 'techniques')
choices = [(t.technique_id, t.name) for t in techniques]
form.fields['peak_techniques'].choices = choices
return form
def export_PSFM(meta_sites, **kwargs):
"""Exports Position-Specific-Frequency-Matrix"""
format = kwargs['format']
rows = export_base(meta_sites)
aligned = lasagna.lasagna([m.delegate_site_instance for m in meta_sites])
motif = bioutils.build_motif(aligned)
consensus = motif.degenerate_consensus
TF_name= ','.join(set(row['TF_name'] for row in rows))
sp = ','.join(set('_'.join(row['organism'].split()) for row in rows))
lines = []
if format == 'JASPAR':
lines.append('> CollecTF_%s_%s' % (TF_name, sp))
lines.append('A [ %s ]' % (' '.join(map(str, motif.counts['A']))))
lines.append('C [ %s ]' % (' '.join(map(str, motif.counts['C']))))
lines.append('G [ %s ]' % (' '.join(map(str, motif.counts['G']))))
lines.append('T [ %s ]' % (' '.join(map(str, motif.counts['T']))))
elif format == 'TRANSFAC':
lines.append('ID %s' % TF_name)
lines.append('BF %s' % sp)
lines.append('PO\tA\tC\tG\tT')
lines.extend('%02d\t%d\t%d\t%d\t%d\t%s' % (po+1, motif.counts['A'][po],
motif.counts['C'][po],
motif.counts['G'][po],
motif.counts['T'][po],
consensus[po])
for po in range(motif.length))
lines.append('XX')
elif format == 'raw_fasta':
lines.append('>CollecTF_%s_%s' % (TF_name, sp))
lines.extend('%d\t%d\t%d\t%d' % (motif.counts['A'][po],
motif.counts['C'][po],
motif.counts['G'][po],
motif.counts['T'][po])
for po in range(motif.length))
return '\n'.join(lines)
def aligned_sites(self):
"""Aligns all binding sites using LASAGNA."""
site_instances = [meta_site.delegate.site_instance
for meta_site in self.meta_sites
if meta_site.site_type == 'motif_associated']
return lasagna.lasagna(site_instances)