def test_fetch_subdirs():
path = fetch_file(URL, decompress=True, subdir="datacache")
assert path.endswith(FASTA_FILENAME)
# if we change the subdir then data should end up in
# something like /Users/me/Library/Caches/epitopes_test/
other_path = fetch_file(URL, decompress=True, subdir="datacache_test")
assert other_path.endswith(FASTA_FILENAME)
assert other_path != path, other_path
def test_fetch_subdirs():
path = fetch_file(URL, decompress=True, subdir="datacache")
assert path.endswith(FASTA_FILENAME)
# if we change the subdir then data should end up in
# something like /Users/me/Library/Caches/epitopes_test/
other_path = fetch_file(URL, decompress=True, subdir="datacache_test")
assert other_path.endswith(FASTA_FILENAME)
assert other_path != path, other_path
def test_fetch_decompress():
path1 = fetch_file(
URL,
decompress=True, subdir="datacache")
assert path1.endswith(FASTA_FILENAME)
with open(path1, 'r') as f1:
s1 = f1.read()
assert "TCAATTTCGTGCCAG" in s1
def test_fetch_decompress():
for use_wget_if_available in [True, False]:
for timeout in [None, 10**6]:
path1 = fetch_file(URL,
decompress=True,
subdir="datacache",
use_wget_if_available=use_wget_if_available,
timeout=timeout)
assert path1.endswith(FASTA_FILENAME)
with open(path1, 'r') as f1:
s1 = f1.read()
assert "TCAATTTCGTGCCAG" in s1
def test_fetch_decompress():
for use_wget_if_available in [True, False]:
for timeout in [None, 10**6]:
path1 = fetch_file(
URL,
decompress=True,
subdir="datacache",
use_wget_if_available=use_wget_if_available,
timeout=timeout)
assert path1.endswith(FASTA_FILENAME)
with open(path1, 'r') as f1:
s1 = f1.read()
assert "TCAATTTCGTGCCAG" in s1
def transcript_id_to_transcript_name(transcript_id, _table_cache = [None]):
if _table_cache[0] is None:
print ("Fetching Ensembl ID mappings from BioMart %s"
) % _BIOMART_URL_TRANSCRIPT_ID_TO_TRANSCRIPT_NAME
biomart_filename = \
datacache.fetch_file(_BIOMART_URL_TRANSCRIPT_ID_TO_TRANSCRIPT_NAME,
"biomart_transcript_name.tsv")
df = pd.read_csv(biomart_filename, sep='\t')
transcript_ids = df['Ensembl Transcript ID']
transcript_names = df['Associated Transcript Name']
mapping = dict(zip(transcript_ids, transcript_names))
_table_cache[0] = mapping
mapping = _table_cache[0]
return mapping[transcript_id]
def transcript_id_to_gene_id(transcript_id, _table_cache = [None]):
if _table_cache[0] is None:
print ("Fetching Ensembl ID mappings from BioMart %s"
) % _BIOMART_URL_TRANSCRIPT_ID_TO_GENE_ID
biomart_filename = \
datacache.fetch_file(_BIOMART_URL_TRANSCRIPT_ID_TO_GENE_ID,
"biomart_transcript_gene.tsv")
df = pd.read_csv(biomart_filename, sep='\t')
gene_ids = df['Ensembl Gene ID']
transcript_ids = df['Ensembl Transcript ID']
mapping = dict(zip(transcript_ids, gene_ids))
_table_cache[0] = mapping
mapping = _table_cache[0]
return mapping[transcript_id]
def make_blastdb(url, name=None, filename=None, overwrite=False):
"""Download protein sequences and a make blast db. Uses datacache module."""
import datacache
cachedir = datacache.get_data_dir()
blastdb = os.path.join(cachedir, name)
if os.path.exists(blastdb+'.phr') and overwrite==False:
#print ('blast files found')
return blastdb
filename = datacache.fetch_file(url, filename=filename, decompress=True, subdir=None)
#print filename
cmd = 'makeblastdb -dbtype prot -in %s -out %s' %(filename,blastdb)
#print cmd
tmp=subprocess.check_output(cmd, shell=True)
return blastdb
def fetch_fasta_dict(path_or_url):
path = fetch_file(path_or_url)
d = {}
value_buffer = []
key = None
if path.endswith(".gz") or path.endswith(".gzip"):
f = gzip.open(path, "r")
else:
f = open(path, "r")
for line in f.readlines():
if type(line) is bytes:
line = line.decode("ascii")
if line.startswith(">"):
if key is not None:
d[key] = "".join(value_buffer)
value_buffer = []
key = line.split()[0][1:]
else:
value_buffer.append(line.strip())
if key and value_buffer:
d[key] = "".join(value_buffer)
f.close()
return d
def fetch_fasta_dict(path_or_url):
path = fetch_file(path_or_url)
d = {}
value_buffer = []
key = None
if path.endswith(".gz") or path.endswith(".gzip"):
f = gzip.open(path, "r")
else:
f = open(path, "r")
for line in f.readlines():
if type(line) is bytes:
line = line.decode("ascii")
if line.startswith(">"):
if key is not None:
d[key] = "".join(value_buffer)
value_buffer = []
key = line.split()[0][1:]
else:
value_buffer.append(line.strip())
if key and value_buffer:
d[key] = "".join(value_buffer)
f.close()
return d
def fetch_file(url, decompress=True):
return datacache.fetch_file(url, decompress=decompress, subdir="immuno")
def fetch_file(url, decompress = True):
return datacache.fetch_file(url, decompress = decompress, subdir = "immuno")
