def install_blast(base_dir):
"""Deprecated, look into 'home_linux/setup/bioinfo_tools'
On Ubuntu: sudo apt-get install ncbi-blast+
"""
# Default location #
if base_dir is None: base_dir = os.environ.get('HOME', '/') + '/programs/blast/'
# Download from FTP #
ftp_url = "ftp.ncbi.nlm.nih.gov"
ftp_dir = "/blast/executables/blast+/LATEST/"
pattern = 'ncbi-blast-*+-src.zip'
ftp = FTPHost(ftp_url, "anonymous")
ftp.chdir(ftp_dir)
files = ftp.listdir(self.ftp.curdir)
ftp.download(source, dest)
rmtdir = '/modelos/io/produtos/MERGE' # diretorio remoto
for d in days:
year = d[:4]
binfile = 'prec_{0}.bin'.format(d)
ctlfile = 'prec_{0}.ctl'.format(d)
locbinfile = '{0}/{1}/{2}'.format(locdir, year, binfile)
locctlfile = '{0}/{1}/{2}'.format(locdir, year, ctlfile)
if not os.path.exists(locbinfile):
msg = 'File not found: {0}'.format(locbinfile)
print(msg)
rmtbinfile = '{0}/{1}/{2}'.format(rmtdir, year, binfile)
rmtctlfile = '{0}/{1}/{2}'.format(rmtdir, year, ctlfile)
host = FTPHost(hostnm, usernm, passwd)
host.download(rmtbinfile, locbinfile) # remoto, local
host.download(rmtctlfile, locctlfile)
else:
msg = 'File already exists: {0}'.format(locbinfile)
print(msg)
