def upload_to_sra(self):
# Print #
print self.s.short_name
# Connect #
print "Connecting..."
ftp = FTPHost(sra.ftp_server, sra.ftp_login, str(sra.ftp_password))
# Make directory #
print "Making directories..."
ftp.makedirs(self.directory)
# Upload #
dest_path = self.directory + self.name
print "Uploading to '%s' (%s)..." % (dest_path, self.s.p.raw_sff.size)
ftp.upload(self.s.p.raw_sff, dest_path)
# Return #
ftp.close()
def upload_to_ena(self):
# Connect #
print "Connecting..."
ftp = FTPHost(ftp_server, ftp_login, str(ftp_password))
# Gzip if not there yet #
if not self.raw_gz.exists:
self.raw.fwd.gzip_to(self.p.raw_forward_gz)
self.raw.rev.gzip_to(self.p.raw_reverse_gz)
# Make directory #
directory = '/ILLUMITAG/run%03d/pool%02d/sample%02d/'
directory = directory % (self.pool.run_num, self.pool.num, self.num)
print "Making directories..."
ftp.makedirs(directory)
# Upload #
base_path = directory + 'run%03d_pool%02d_sample%02d_{}_reads.fastq.gz'
base_path = base_path % (self.pool.run_num, self.pool.num, self.num)
print "Uploading forward..."
ftp.upload(self.p.raw_forward_gz, base_path.format("forward"))
print "Uploading reverse..."
ftp.upload(self.p.raw_reverse_gz, base_path.format("reverse"))
# Return #
ftp.close()
def upload_to_sra(self, verbose=True):
"""They have an FTP site where you should drop the files first"""
# Print #
if verbose: print self.s.short_name + ' (' + self.s.name + ')'
# Connect #
if verbose: print "Connecting..."
ftp = FTPHost(ftp_server, ftp_login, str(ftp_password))
# Gzip if not there yet #
if not self.s.raw_gz.exists:
self.s.raw.fwd.gzip_to(self.s.p.raw_forward_gz)
self.s.raw.rev.gzip_to(self.s.p.raw_reverse_gz)
# Make directory #
if verbose: print "Making directories..."
ftp.makedirs(self.directory)
# Upload #
base_path = self.directory + self.base_name
if verbose: print "Uploading forward..."
ftp.upload(self.s.p.raw_forward_gz, base_path.format("forward"))
if verbose: print "Uploading reverse..."
ftp.upload(self.s.p.raw_reverse_gz, base_path.format("reverse"))
# Return #
ftp.close()
