def list_raw(self, sample_names=None, city_name=None, project_name=None, grouped=False):
"""List raw read files, from a given city if specified."""
samples = set()
if city_name or project_name:
samples |= set(get_samples_from_city(city_name, project_name=project_name))
if sample_names:
samples |= set(sample_names)
raw_reads = {
key.key
for key in self.bucket.objects.filter(Prefix='data')
if key.key[-9:] == '.fastq.gz'
}
raw_read_files = {}
for raw_read in raw_reads:
sname = basename(raw_read).split('_1.fastq.gz')[0].split('_2.fastq.gz')[0]
if samples and sname not in samples:
continue
raw_read_files[sname] = sorted([raw_read] + raw_read_files.get(sname, []))
raw_list = []
for read_files in raw_read_files.values():
if not grouped:
raw_list += read_files
else:
raw_list.append(read_files)
return raw_list
def list_contigs(self,
sample_names=None, city_name=None, project_name=None,
contig_file='scaffolds.fasta'):
"""List all the contigs."""
samples = set()
if city_name or project_name:
samples |= set(get_samples_from_city(city_name, project_name=project_name))
if sample_names:
samples |= set(sample_names)
contigs = [
key.key
for key in self.bucket.objects.all()
if 'assemblies' in key.key and contig_file == basename(key.key)
]
if samples:
contigs = [el for el in contigs if basename(dirname(el)).split('.')[0] in samples]
return contigs
def nonhuman_reads(sample_names=None, city_name=None, project_name=None):
samples = set()
if city_name or project_name:
samples |= set(get_samples_from_city(city_name, project_name=project_name))
if sample_names:
samples |= set(sample_names)
nonhuman_reads = [
filename for filename in list_public_files()
if 'nonhuman_read' in filename and '/human_filtered_data/' in filename
]
nonhuman_read_files = {}
for nonhuman_read in nonhuman_reads:
sname = basename(nonhuman_read).split('.')[0]
if samples and sname not in samples:
continue
nonhuman_read_files[sname] = sorted([nonhuman_read] + nonhuman_read_files.get(sname, []))
return nonhuman_read_files
def test_get_samples_from_city_project(self):
"""Test that we can filter sample names by city and project."""
sample_names = get_samples_from_city('swansea', project_name='tigress')
self.assertTrue(len(sample_names) == 6)
def test_get_samples_from_project(self):
"""Test that we can filter sample names by project."""
sample_names = get_samples_from_city(None, project_name='tigress')
self.assertTrue(len(sample_names) == 83)
def test_get_samples_from_city(self):
"""Test that we get some sample names from a city (assume correct)."""
sample_names = get_samples_from_city('paris')
self.assertTrue(sample_names)