def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('sample_list'):
indiv_id_list = []
for line in open(options.get('sample_list')):
if line.strip() == "" or line.startswith('#'):
continue
indiv_id_list.append(line.strip())
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('vcf'):
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('ped'):
fam_file = open(options.get('ped'))
sample_management.update_project_from_fam(project, fam_file)
def handle(self, *args, **options):
if len(args)==0 or options['vcf'] is None and options['ped'] is None and options['xls'] is None:
print '\n\nPlease enter a VCF file (--vcf), OR IDEALLY A PED or XLS file (using --ped or --xls), and a project ID (first positional argument).'
print 'For example: python manage.py add_individuals_to_project myProjectId --ped myPed.ped\n'
sys.exit()
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('sample_list'):
if options.get('case_review'):
raise ValueError("--case-review not supported for sample list")
indiv_id_list = []
for line in open(options.get('sample_list')):
if line.strip() == "" or line.startswith('#'):
continue
indiv_id_list.append(line.strip())
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('vcf'):
if options.get('case_review'):
raise ValueError("--case-review not supported for vcf")
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('ped'):
in_case_review = options.get('case_review')
fam_file = options.get('ped')
fam_stuff.validate_fam_file(open(fam_file))
individual_details = sample_management.update_project_from_fam(project, open(fam_file),
in_case_review=in_case_review)
for j in individual_details:
print("Adding %s: %s" % (j['indiv_id'], j))
if options.get('xls'):
in_case_review = options.get('case_review')
xls_file = options.get('xls')
title_row, xl_rows = parse_xl_workbook(xls_file)
temp_ped_filename = 'temp.ped'
write_xl_rows_to_ped(temp_ped_filename, xl_rows)
fam_stuff.validate_fam_file(open(temp_ped_filename))
individual_details = sample_management.update_project_from_fam(project, open(temp_ped_filename),
in_case_review=in_case_review)
#for j in individual_details:
# print("Adding %s: %s" % (j['indiv_id'], j))
def handle(self, *args, **options):
if len(args)==0 or options['vcf'] is None and options['ped'] is None and options['xls'] is None:
print '\n\nPlease enter a VCF file (--vcf), OR IDEALLY A PED or XLS file (using --ped or --xls), and a project ID (first positional argument).'
print 'For example: python manage.py add_individuals_to_project myProjectId --ped myPed.ped\n'
sys.exit()
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('sample_list'):
if options.get('case_review'):
raise ValueError("--case-review not supported for sample list")
indiv_id_list = []
for line in open(options.get('sample_list')):
if line.strip() == "" or line.startswith('#'):
continue
indiv_id_list.append(line.strip())
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('vcf'):
if options.get('case_review'):
raise ValueError("--case-review not supported for vcf")
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('ped'):
in_case_review = options.get('case_review')
fam_file = options.get('ped')
fam_stuff.validate_fam_file(open(fam_file))
individual_details = sample_management.update_project_from_fam(project, open(fam_file),
in_case_review=in_case_review)
for j in individual_details:
print("Adding %s: %s" % (j['indiv_id'], j))
if options.get('xls'):
in_case_review = options.get('case_review')
xls_file = options.get('xls')
title_row, xl_rows = parse_xl_workbook(xls_file)
temp_ped_filename = 'temp.ped'
write_xl_rows_to_ped(temp_ped_filename, xl_rows)
fam_stuff.validate_fam_file(open(temp_ped_filename))
individual_details = sample_management.update_project_from_fam(project, open(temp_ped_filename),
in_case_review=in_case_review)
def handle(self, *args, **options):
if len(args)==0 or options['vcf'] is None and options['ped'] is None:
print '\n\nPlease enter a VCF file (--vcf), OR IDEALLY A PED file (--ped), and a project ID (first positional argument).'
print 'For example: python manage.py add_individuals_to_project myProjectId --ped myPed.ped\n'
print 'If you also wish to create patients in phenotips, please use the --create_phenotips_patients\n'
sys.exit()
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('sample_list'):
indiv_id_list = []
for line in open(options.get('sample_list')):
if line.strip() == "" or line.startswith('#'):
continue
indiv_id_list.append(line.strip())
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('vcf'):
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('ped'):
fam_file = open(options.get('ped'))
individual_details = sample_management.update_project_from_fam(project, fam_file)
def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir,
project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify(s, separator='_') for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(
project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(
file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
def handle(self, *args, **options):
project_id = args[0]
project = Project.objects.get(project_id=project_id)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir, project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify.slugify(s) for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
def handle(self, *args, **options):
if (options['vcf'] is None and options['ped'] is None) or len(args)==0:
print '\n\nPlease enter a VCF file (--vcf) or a PED file (--ped), and a project ID (first positional argument)'
print 'for example: python manage.py add_individuals_to_project myProjectId --ped myPed.ped\n'
print 'If you also wish to create patients in phenotips, please use the --create_phenotips_patients,--phenotips_username, --phenotips_password to do so. ALL of them are REQUIRED.\n'
sys.exit()
if options['create_phenotips_patients'] is not None and (options['phenotips_username'] is None or options['phenotips_password'] is None):
print '\n\nplease note if you use the --create_phenotips_patients option, both --phenotips_username and --phenotips_password options are REQUIRED.\n\n'
sys.exit()
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('sample_list'):
indiv_id_list = []
for line in open(options.get('sample_list')):
if line.strip() == "" or line.startswith('#'):
continue
indiv_id_list.append(line.strip())
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('vcf'):
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
self.__add_individuals_to_phenotips(indiv_id_list)
sample_management.add_indiv_ids_to_project(project, indiv_id_list)
if options.get('ped'):
fam_file = open(options.get('ped'))
sample_management.update_project_from_fam(project, fam_file)
def handle(self, *args, **options):
'''
Handles populating Phenotips.
Currently favors PED file for richer set of information (vs VCF) to create patients
'''
if len(args)==0 or options['vcf'] is None and options['ped'] is None:
print '\n\nAdds a series of patients to Phenotips.\n'
print 'Please enter a VCF file (--vcf), OR IDEALLY A PED file (--ped), and a project ID (first positional argument).'
print 'For example: python manage.py add_individuals_to_phenotips myProjectId --ped myPed.ped\n'
sys.exit()
project_id = args[0]
project = Project.objects.get(project_id=project_id)
if options.get('vcf') and not os.path.exists(options.get('vcf')):
print '\n\nError: the VCF file you entered does not exist or is invalid\n\n'
sys.exit()
if options.get('ped') and not os.path.exists(options.get('ped')):
print '\n\nError: the PED file you entered does not exist or is invalid\n\n'
sys.exit()
indiv_id_list=None
if options.get('vcf'):
vcf_path = options.get('vcf')
if vcf_path.endswith('.gz'):
vcf = gzip.open(vcf_path)
else:
vcf = open(vcf_path)
indiv_id_list = vcf_stuff.get_ids_from_vcf(vcf)
individual_details=None
if options.get('ped'):
fam_file = open(options.get('ped'))
individual_details = sample_management.update_project_from_fam(project, fam_file)
if individual_details is not None:
add_individuals_to_phenotips_from_ped(individual_details,project_id)
else:
if indiv_id_list is not None:
add_individuals_to_phenotips_from_vcf(indiv_id_list,project_id)
else:
print '\n\nWARNING: No information was found in VCF to create patients with\n'
sys.exit()
def handle(self, *args, **options):
project = Project.objects.get(project_id=options.get('project_id'))
fam_file = open(options.get('fam_file'))
sample_management.update_project_from_fam(project, fam_file)
def handle(self, *args, **options):
if len(args) < 2:
print("Usage: ./manage.py load_project_dir <project_id> <project_path>")
print("")
sys.exit(1)
project_id = args[0]
try:
project = Project.objects.get(project_id=project_id)
except Project.DoesNotExist:
print("\nError:")
print("\nNo project could be found with id '%s'" % project_id)
print("")
print("Please use the add_project command first to add this project before loading it.")
print("")
sys.exit(1)
project_dir = os.path.abspath(args[1])
project_yaml_file = os.path.join(project_dir, 'project.yaml')
project_spec = yaml.load(open(project_yaml_file))
# load in sample IDs that we'll use for the project
sample_id_file = os.path.join(project_dir, project_spec['sample_id_list'])
sample_ids = [l.strip('\n') for l in open(sample_id_file)]
sample_ids = [slugify(s, separator='_') for s in sample_ids]
sample_management.add_indiv_ids_to_project(project, sample_ids)
# set meta info
project.project_name = project_spec['project_name']
project.save()
# nicknames
if 'nicknames' in project_spec:
# todo
pass
# load individuals
if 'ped_files' in project_spec:
for relative_path in project_spec['ped_files']:
ped_file_path = os.path.join(project_dir, relative_path)
sample_management.update_project_from_fam(project, open(ped_file_path))
# todo: add awesome-slugify to above
# set VCF files
if 'vcf_files' in project_spec:
for relative_path in project_spec['vcf_files']:
vcf_file_path = os.path.join(project_dir, relative_path)
# todo: this should be a fn somewhere that add_vcf_to_project uses too
vcf_file = VCFFile.objects.get_or_create(file_path=vcf_file_path)[0]
sample_management.add_vcf_file_to_project(project, vcf_file)
if 'breakpoint_files' in project_spec:
for relative_path in project_spec['breakpoint_files']:
breakpoint_file = BreakpointFile()
breakpoint_file.project = project
breakpoint_file.file_path = os.path.join(project_dir, relative_path)
breakpoint_file.save()
print("Adding breakpoint file: %s" % breakpoint_file.file_path)
def handle(self, *args, **options):
project = Project.objects.get(project_id=options.get('project_id'))
fam_file = open(options.get('fam_file'))
sample_management.update_project_from_fam(project, fam_file)
