def refresh_cache(self):
"""Will download the required zip files to the cache directory."""
download_from_url(self.url,
self.zip_path,
stream=True,
progress=True,
uncompress=False)
def install(cls, prefix="~/programs/fastQValidator/"):
"""
To automatically download and install the fastQValidator software
on this computer and for the current user, type these commands in
python:
>>> from fasta.validator import Validator
>>> Validator.install()
"""
# Check we are on an OS with aptitude #
check_apt_exists()
# Start with the required apt packages #
get_apt_packages(cls.apt_packages, verbose=True)
# Download tarball 1 #
tmp_dir_1 = new_temp_dir()
tgz_url_1 = 'https://github.com/statgen/libStatGen/archive/master.tar.gz'
tgz_loc_1 = download_from_url(tgz_url_1,
tmp_dir_1,
stream=True,
progress=True)
src_dir_1 = tgz_loc_1.untargz_to()
# Download tarball 2 #
tmp_dir_2 = new_temp_dir()
tgz_url_2 = 'https://github.com/statgen/fastQValidator/archive/master.tar.gz'
tgz_loc_2 = download_from_url(tgz_url_2,
tmp_dir_2,
stream=True,
progress=True)
src_dir_2 = tgz_loc_2.untargz_to()
# Uncompressed 1 #
src_dir_1 = src_dir_1.sub_directory
# Uncompressed 2 #
src_dir_2 = src_dir_2.sub_directory
# Make 1 #
sh.make('-C', src_dir_1, _out=sys.stdout, _err=sys.stderr)
# Make 2 #
sh.make(
'-C',
src_dir_2,
'LIB_PATH_FASTQ_VALIDATOR=%s' % src_dir_1,
_out=sys.stdout,
_err=sys.stderr,
)
# Move the executable #
binary = src_dir_2 + 'bin/fastQValidator'
path = binary.move_to(prefix, overwrite=True)
# The directory that contains the executable #
bin_dir = path.directory.with_tilda[:-1].replace('~', '$HOME')
# Suggest adding to the $PATH #
print("\n fastQValidator was installed successfully. You should now "
"add this line to your .bash_profile: \n\n "
"export PATH=%s:$PATH\n" % bin_dir)
def prepare(self):
"""Check that the file exists, optionally downloads it.
Checks that the file is indeed an SQLite3 database.
Optionally check the MD5."""
if not os.path.exists(self.path):
if self.retrieve:
print("Downloading SQLite3 database...")
download_from_url(self.retrieve, self.path, progress=True)
else:
raise Exception("The file '" + self.path + "' does not exist.")
self.check_format()
if self.known_md5: assert self.known_md5 == self.md5
self.prepared = True
def refresh_cache(self):
"""Will download the required zip files to the cache directory."""
return download_from_url(self.base_url + self.url_param,
self.zip_path,
stream=False,
progress=False,
uncompress=False)
def install(cls, prefix="~/programs/FastQC/"):
"""
To automatically download and install the FastQC software on this
computer and for the current user, type these commands in python:
>>> from fasta.fastqc import FastQC
>>> FastQC.install()
"""
# Start with required apt packages #
get_apt_packages(cls.apt_packages, verbose=True)
# Make a temporary directory #
tmp_dir = new_temp_dir()
# Download tarball #
zip_loc = download_from_url(cls.zip_url, tmp_dir, stream=True,
progress=True)
# Uncompress #
src_dir = zip_loc.unzip_to(prefix, single=False).sub_directory
# Set executable permissions #
bin_loc = src_dir + 'fastqc'
bin_loc.permissions.make_executable()
# The directory that contains the executable #
bin_dir = src_dir.with_tilda[:-1].replace('~', '$HOME')
# Suggest adding to the $PATH #
print("\nFastQC was installed successfully. You should now "
"add this line to your .bash_profile: \n\n "
"export PATH=%s:$PATH\n" % bin_dir)
def get_one_xls(self, row):
"""Download one xls file and put it in the cache directory."""
# We are not interested in all countries #
if row['country'] not in country_codes['country'].values: return
# Get the matching iso2_code #
iso2_code = country_codes.query("country == '%s'" % row['country'])
iso2_code = iso2_code['iso2_code'].iloc[0]
# The destination directory #
destination = Path(self.cache_dir + iso2_code + '.xls')
# Save to disk #
result = download_from_url(row['xls'], destination, user_agent=None)
# We don't want to flood the server #
time.sleep(2)
# Return #
return result