def prepare(args):
try:<EOL><INDENT>f = open(args.config, '<STR_LIT:r>')<EOL>seq_out = open(op.join(args.out, "<STR_LIT>"), '<STR_LIT:w>')<EOL>ma_out = open(op.join(args.out, "<STR_LIT>"), '<STR_LIT:w>')<EOL><DEDENT>except IOError as e:<EOL><INDENT>traceback.print_exc()<EOL>raise IOError("<STR_LIT>" % (op.join(args.out, "<STR_LIT>"), op.join(args.out, "<STR_LIT>"), args.config))<EOL><DEDENT>logger.info("<STR_LIT>")<EOL>seq_l, sample_l = _read_fastq_files(f, args)<EOL>logger.info("<STR_LIT>")<EOL>logger.info("<STR_LIT>" % (args.minc, args.minl, args.maxl, args.min_shared))<EOL>_create_matrix_uniq_seq(sample_l, seq_l, ma_out, seq_out, args.min_shared)<EOL>logger.info("<STR_LIT>")<EOL>
Read all seq.fa files and create a matrix and unique fasta files.
The information is

:param args: options parsed from command line
:param con: logging messages going to console
:param log: logging messages going to console and file

:returns: files - matrix and fasta files that should be used with
 and aligner (as bowtie) and run `seqcluster cluster`