"'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)
