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()