From b523d132d67da71c778323b7c50e8a8b4597a651 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20=20MENAGER?= <herve.menager@pasteur.fr>
Date: Thu, 18 May 2017 16:08:54 +0200
Subject: [PATCH] migrate Ppi and PpiComplex data
fixes #24
---
ippisite/db.sqlite3 | Bin 569344 -> 569344 bytes
.../management/commands/import_v1_data.py | 100 +++++++++++-------
.../migrations/0011_auto_20170518_1404.py | 20 ++++
ippisite/ippidb/models.py | 2 +-
4 files changed, 81 insertions(+), 41 deletions(-)
create mode 100644 ippisite/ippidb/migrations/0011_auto_20170518_1404.py
diff --git a/ippisite/db.sqlite3 b/ippisite/db.sqlite3
index 585c05bac9b5bb713a7f404b36981aaa02f2ba17..8222fa0613fb7defe327ce8452ea41e836d26eeb 100644
GIT binary patch
delta 6316
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diff --git a/ippisite/ippidb/management/commands/import_v1_data.py b/ippisite/ippidb/management/commands/import_v1_data.py
index 67b83282..69948d26 100644
--- a/ippisite/ippidb/management/commands/import_v1_data.py
+++ b/ippisite/ippidb/management/commands/import_v1_data.py
@@ -2,7 +2,7 @@ from django.core.management import BaseCommand, CommandError
import mysql.connector
from ippidb.models import Bibliography, Protein, Taxonomy, MolecularFunction, \
- Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi
+ Domain, ProteinDomainBoundComplex, ProteinDomainPartnerComplex, Symmetry, Ppi, PpiComplex
class Command(BaseCommand):
@@ -31,18 +31,18 @@ class Command(BaseCommand):
help='Flush and migrate domains',
)
parser.add_argument(
- '--complexes',
+ '--symmetries',
action='store_true',
- dest='complexes',
+ dest='symmetries',
default=False,
- help='Flush and migrate complexes',
+ help='Flush and create symmetries',
)
parser.add_argument(
- '--symmetries',
+ '--ppi',
action='store_true',
- dest='symmetries',
+ dest='ppi',
default=False,
- help='Flush and create symmetries',
+ help='Flush and migrate ppis and complexes',
)
parser.add_argument(
'--stoponfail',
@@ -117,39 +117,6 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[1], row[2])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[1], row[2])))
- if options['complexes']:
- sql_request_string = '''
- select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) union select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)'''
- cursor.execute(sql_request_string)
- rows = cursor.fetchall()
- ProteinDomainBoundComplex.objects.all().delete()
- ProteinDomainPartnerComplex.objects.all().delete()
- Ppi.objects.all().delete()
- self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables and Ppi'))
- for row in rows:
- try:
- if row[3]=="null":
- c = ProteinDomainPartnerComplex()
- else:
- c = ProteinDomainBoundComplex()
- protein = Protein.objects.get(uniprot_id=row[0])
- c.protein_id = protein
- domain = Domain.objects.get(pfam_acc=row[1])
- c.domain_id = domain
- c.ppc_copy_nb = row[2]
- if isinstance(c, ProteinDomainBoundComplex):
- c.ppp_copy_nb_per_p = 1
- c.pockets_nb = 1
- c.save()
- except Exception as e:
- if options['stoponfail']:
- import traceback
- self.stderr.write(traceback.format_exc())
- raise CommandError('Failed inserting {} {}'.format(row[0], row[1]))
- else:
- self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
- else:
- self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
if options['symmetries']:
Symmetry.objects.all().delete()
self.stdout.write(self.style.SUCCESS('Successfully flushed symmetries table'))
@@ -179,4 +146,57 @@ class Command(BaseCommand):
self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
else:
self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
+ if options['ppi']:
+ sql_request_string = '''
+select distinct protein.NumUniprot, domain.PfamNumAccession, complexe.NbCopy, cmpdAction.IDComplexeBound, bindingSiteEvidence.CodePDB, 'part1', ppi.IDPPI from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite1) inner join complexe on (ppi.IDComplexe1=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain) left outer join bindingSiteEvidence on (ppi.IDPPI=bindingSiteEvidence.IDPPI)
+union
+select distinct protein.NumUniprot, domain.PfamNumAccession , complexe.NbCopy, cmpdAction.IDComplexeBound, null, 'part2', ppi.IDPPI from bindingSite inner join ppi on (bindingSite.IDBindingSite=ppi.IDBindingSite2) inner join complexe on (ppi.IDComplexe2=complexe.IDComplexe) left outer join cmpdAction on (complexe.IDComplexe=cmpdAction.IDComplexeBound) inner join protein on (bindingSite.IDProtein=protein.IDProtein) inner join domain on (bindingSite.IDDomain=domain.IDDomain)'''
+ cursor.execute(sql_request_string)
+ rows = cursor.fetchall()
+ ProteinDomainBoundComplex.objects.all().delete()
+ ProteinDomainPartnerComplex.objects.all().delete()
+ Ppi.objects.all().delete()
+ PpiComplex.objects.all().delete()
+ self.stdout.write(self.style.SUCCESS('Successfully flushed protein domain complex tables and Ppi'))
+ ppi_ids_mapping = {}
+ for row in rows:
+ try:
+ # create or retrieve Ppi object
+ if row[5]=='part1':
+ ppi = Ppi()
+ ppi.pdb_id = row[4]
+ ppi.symmetry = Symmetry.objects.get(code='AS')
+ ppi.save()
+ ppi_ids_mapping[row[6]]=ppi.id
+ else:
+ ppi = Ppi.objects.get(id=ppi_ids_mapping[row[6]])
+ # create a complex
+ if row[3]=="null":
+ c = ProteinDomainPartnerComplex()
+ else:
+ c = ProteinDomainBoundComplex()
+ protein = Protein.objects.get(uniprot_id=row[0])
+ c.protein = protein
+ domain = Domain.objects.get(pfam_acc=row[1])
+ c.domain = domain
+ c.ppc_copy_nb = row[2]
+ if isinstance(c, ProteinDomainBoundComplex):
+ c.ppp_copy_nb_per_p = 1
+ c.pockets_nb = 1
+ c.save()
+ # create the PpiComplex object
+ ppi_complex = PpiComplex()
+ ppi_complex.ppi = ppi
+ ppi_complex.complex = c
+ ppi_complex.cc_nb = 1
+ ppi_complex.save()
+ except Exception as e:
+ if options['stoponfail']:
+ import traceback
+ self.stderr.write(traceback.format_exc())
+ raise CommandError('Failed inserting {} {}'.format(row[0], row[1]))
+ else:
+ self.stdout.write(self.style.ERROR('Failed inserting {} {}'.format(row[0], row[1])))
+ else:
+ self.stdout.write(self.style.SUCCESS('Successfully inserted {} {}'.format(row[0], row[1])))
diff --git a/ippisite/ippidb/migrations/0011_auto_20170518_1404.py b/ippisite/ippidb/migrations/0011_auto_20170518_1404.py
new file mode 100644
index 00000000..9abe3d73
--- /dev/null
+++ b/ippisite/ippidb/migrations/0011_auto_20170518_1404.py
@@ -0,0 +1,20 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.1 on 2017-05-18 14:04
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+ dependencies = [
+ ('ippidb', '0010_auto_20170518_1142'),
+ ]
+
+ operations = [
+ migrations.AlterField(
+ model_name='ppi',
+ name='pdb_id',
+ field=models.CharField(max_length=4, null=True, verbose_name='PDB ID'),
+ ),
+ ]
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 50288a93..4e4f0901 100644
--- a/ippisite/ippidb/models.py
+++ b/ippisite/ippidb/models.py
@@ -150,7 +150,7 @@ class Symmetry(models.Model):
return '{} ({})'.format(self.code, self.description)
class Ppi(models.Model):
- pdb_id = models.CharField('PDB ID', max_length=4)
+ pdb_id = models.CharField('PDB ID', max_length=4, null=True)
symmetry = models.ForeignKey(Symmetry)
class PpiComplex(models.Model):
--
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