"'NY_ChIP-seq'. Use multiple --expt=... to set the types for different " "projects") p.add_option("--keep-names",action="store_true",dest="keep_names",default=False, help="preserve the full names of the source fastq files when creating links") p.add_option("--merge-replicates",action="store_true",dest="merge_replicates",default=False, help="create merged fastq files for each set of replicates detected") # Parse command line options,args = p.parse_args() # Get data directory name if len(args) != 1: p.error("expected one argument (location of Illumina analysis dir)") illumina_analysis_dir = os.path.abspath(args[0]) # Populate Illumina data object illumina_data = IlluminaData.IlluminaData(illumina_analysis_dir, unaligned_dir=options.unaligned_dir) # Assign experiment types for expt in options.expt_type: name,type_ = expt.split(':') illumina_data.get_project(name).expt_type = type_ # Create and populate per-project directory structure for project in illumina_data.projects: create_analysis_dir(project, top_dir=illumina_analysis_dir, merge_replicates=options.merge_replicates, keep_names=options.keep_names, dry_run=options.dry_run)