def db_dump():
"""Generates the release file containing all binding sites in CollecTF."""
curation_site_instances = models.Curation_SiteInstance.objects.all()
reports = motif_report.build_motif_reports(curation_site_instances)
meta_sites = [meta_site
for report in reports
for meta_site in report.meta_sites]
tsv_raw = export.export_tsv(meta_sites)
export_file = os.path.join(
settings.STATICFILES_DIRS[0], 'collectf_export.tsv')
with open(export_file, 'w') as f:
f.write(tsv_raw)
def db_dump():
"""Generates the release file containing all binding sites in CollecTF."""
curation_site_instances = models.Curation_SiteInstance.objects.all()
reports = motif_report.build_motif_reports(curation_site_instances)
meta_sites = [
meta_site for report in reports for meta_site in report.meta_sites
]
tsv_raw = export.export_tsv(meta_sites)
export_file = os.path.join(settings.STATICFILES_DIRS[0],
'collectf_export.tsv')
with open(export_file, 'w') as f:
f.write(tsv_raw)
def generate_uniprot_dbxref():
export_file = os.path.join(settings.STATICFILES_DIRS[0], "uniprot_dbxref.txt")
with open(export_file, "w") as f:
for TF_instance in models.TFInstance.objects.all():
print TF_instance
reports = motif_report.build_motif_reports(
models.Curation_SiteInstance.objects.filter(curation__TF_instances=TF_instance)
)
if reports:
f.write(
"\t".join([TF_instance.uniprot_accession, dbxref.to_uniprot_dbxref(TF_instance.TF_instance_id)])
)
f.write("\n")
def all_alignments():
"""Generates aligned binding moitfs."""
curation_site_instances = models.Curation_SiteInstance.objects.all()
reports = motif_report.build_motif_reports(curation_site_instances)
zip_file_name = os.path.join(settings.STATICFILES_DIRS[0],
'collectf_alignments.zip')
with ZipFile(zip_file_name, 'w') as zip:
for report in reports:
if len(report.aligned_sites) >= 8:
tf = report.TF_name
species = report.short_species_name.replace('.', '_')
print tf, species
filename = '%s_%s.txt' % (tf, species)
zip.writestr(filename, '\n'.join(report.aligned_sites))
def generate_uniprot_dbxref():
export_file = os.path.join(settings.STATICFILES_DIRS[0],
'uniprot_dbxref.txt')
with open(export_file, 'w') as f:
for TF_instance in models.TFInstance.objects.all():
print TF_instance
reports = motif_report.build_motif_reports(
models.Curation_SiteInstance.objects.filter(
curation__TF_instances=TF_instance))
if reports:
f.write('\t'.join(
[TF_instance.uniprot_accession,
dbxref.to_uniprot_dbxref(TF_instance.TF_instance_id)]))
f.write('\n')
def all_alignments():
"""Generates aligned binding moitfs."""
curation_site_instances = models.Curation_SiteInstance.objects.all()
reports = motif_report.build_motif_reports(curation_site_instances)
zip_file_name = os.path.join(settings.STATICFILES_DIRS[0],
'collectf_alignments.zip')
with ZipFile(zip_file_name, 'w') as zip:
for report in reports:
if len(report.aligned_sites) >= 8:
tf = report.TF_name
species = report.short_species_name.replace('.', '_')
print tf, species
filename = '%s_%s.txt' % (tf, species)
zip.writestr(filename, '\n'.join(report.aligned_sites))
def generate_motif_file():
"""Generates motif file containing all motifs for each TF-instance."""
export_file = os.path.join(settings.STATICFILES_DIRS[0],
'collectf_meme.cm')
with open(export_file, 'w') as f:
for TF_instance in models.TFInstance.objects.all():
print TF_instance
reports = motif_report.build_motif_reports(
models.Curation_SiteInstance.objects.filter(
curation__TF_instances=TF_instance))
if reports:
sites = reports[0].aligned_sites
if len(sites) < 10:
continue
motif = build_motif(sites)
f.write('>%s %s_%s\n' % (
dbxref.to_uniprot_dbxref(TF_instance.TF_instance_id),
reports[0].TF_name,
reports[0].short_species_name))
f.write('%s\n' % '\t'.join(map(str, motif.counts['A'])))
f.write('%s\n' % '\t'.join(map(str, motif.counts['C'])))
f.write('%s\n' % '\t'.join(map(str, motif.counts['G'])))
f.write('%s\n' % '\t'.join(map(str, motif.counts['T'])))