def suggest_analysis_layout(solid_runs):
"""Generate a bash script to build the analysis directory scheme
Given a set of SolidRuns, print a set of script commands for running the
build_analysis_dir.py program to create and populate the analysis directories.
The script can be edited before being executed by the user.
Arguments:
solid_runs: a list of SolidRun objects.
"""
print("#!/bin/sh\n#\n# Script commands to build analysis directory structure")
for run in solid_runs:
build_analysis_dir_cmd = 'build_analysis_dir.py'
top_dir = os.path.abspath(os.path.join(os.getcwd(),os.path.basename(run.run_dir)))
for sample in run.samples:
for project in sample.projects:
# Create one experiment per project
cmd_line = []
expt = Experiment.Experiment()
expt.name = project.getProjectName()
expt.type = "expt"
expt.sample = project.getSample().name
expt.library = project.getLibraryNamePattern()
# Print the arguments for the layout
cmd_line.extend((build_analysis_dir_cmd,
"--top-dir=%s_analysis" % top_dir,
"--link=absolute",
"--naming-scheme=partial"))
cmd_line.append(expt.describe())
cmd_line.append(run.run_dir)
print("#\n%s" % (' \\\n').join(cmd_line))
print " each experiment."
print ""
print "For each experiment defined on the command line, a subdirectory"
print "called '<name>_<expt_type>' (e.g. 'PB_ChIP-seq' - if no <expt_type>"
print "was supplied then just the name is used) will be made, and links to"
print "each of the primary data files."
sys.exit(1)
# Solid run directory
solid_run_dir = sys.argv[-1]
if not os.path.isdir(solid_run_dir):
logging.error("Solid run directory '%s' not found" % solid_run_dir)
sys.exit(1)
# Set up experiment list
expts = Experiment.ExperimentList(solid_run_dir=solid_run_dir)
# Process command line arguments
for arg in sys.argv[1:-1]:
# Process command line arguments
if arg.startswith('--name='):
expt_name = arg.split('=')[1]
expt = expts.addExperiment(expt_name)
elif arg.startswith('--type='):
expt = expts.getLastExperiment()
if expt is None:
logging.error("No experiment defined for --type argument")
sys.exit(1)
if not expt.type:
expt.type = arg.split('=')[1]
else: