#!/usr/bin/env python2 """ the main CLI for calling ipyrad """ from __future__ import print_function, division # Requires Python 2.7+ from ipyrad.core.parallel import ipcontroller_init from ipyrad.assemble.util import IPyradError, IPyradWarningExit import pkg_resources import ipyrad as ip import argparse import logging import sys import os # pylint: disable=W0212 LOGGER = logging.getLogger(__name__) def parse_params(args): """ Parse the params file args, create and return Assembly object.""" ## check that params.txt file is correctly formatted. try: with open(args.params) as paramsin: plines = paramsin.readlines() except IOError as _: sys.exit("No params file found") ## check header: big version changes can be distinguished by the header assert len(plines[0].split()[0]) == 6, \ "params file is not compatible with ipyrad v.{}.".format(ip.__version__) \ + "Create a new params file with: ipyrad -n" ## check length ## assert len(plines) > 30, "params file error. Format not recognized." ## make into a dict items = [i.split("##")[0].strip() for i in plines[1:]] #keys = [i.split("]")[-2][-1] for i in plines[1:]] keys = range(len(plines)-1) parsedict = {str(i):j for i, j in zip(keys, items)} return parsedict def showstats(parsedict): """ loads assembly or dies, and print stats to screen """ project_dir = parsedict['1'] ## Be nice if somebody also puts in the file extension assembly_name = parsedict['0'] my_assembly = os.path.join(project_dir, assembly_name) ## If the project_dir doesn't exist don't even bother trying harder. if not os.path.isdir(project_dir): msg = """ Trying to print stats for a project dir ({}) that doesn't exist. You must run steps before you can show stats. """.format(project_dir) sys.exit(msg) if not assembly_name: msg = """ Assembly name is not set in params.txt, meaning it was either changed or erased since the Assembly was started. Please restore the original name. You can find the name of your Assembly in the "project dir": {}. """.format(project_dir) raise IPyradError(msg) data = ip.load_json(my_assembly, quiet=True) print("\nSummary stats of Assembly {}".format(data.name) \ +"\n------------------------------------------------") if not data.stats.empty: print(data.stats) print("\n\nFull stats files"\ +"\n------------------------------------------------") fullcurdir = os.path.realpath(os.path.curdir) for i in range(1,8): #enumerate(sorted(data.stats_files)): key = "s"+str(i) try: val = data.stats_files[key] val = val.replace(fullcurdir, ".") print("step {}: {}".format(i, val)) except (KeyError, AttributeError): print("step {}: None".format(i)) print("\n") else: print("No stats to display") def branch_assembly(args, parsedict): """ Load the passed in assembly and create a branch. Copy it to a new assembly, and also write out the appropriate params.txt """ ## Get the current assembly data = getassembly(args, parsedict) new_data = data.branch(args.branch) print(" Creating a branch of assembly {} called {}".\ format(data.name, new_data.name)) print(" Writing new params file to {}"\ .format("params-"+new_data.name+".txt")) new_data.write_params("params-"+new_data.name+".txt") def getassembly(args, parsedict): """ loads assembly or creates a new one and set its params from parsedict. Does not launch ipcluster. """ ## Creating an assembly with a full path in the name will "work" ## but it is potentially dangerous, so here we have assembly_name ## and assembly_file, name is used for creating new in cwd, file is ## used for loading existing. ## ## Be nice if the user includes the extension. project_dir = ip.core.assembly.expander(parsedict['1']) assembly_name = parsedict['0'] assembly_file = os.path.join(project_dir, assembly_name) ## Assembly creation will handle error checking on ## the format of the assembly_name ## make sure the working directory exists. if not os.path.exists(project_dir): os.mkdir(project_dir) try: ## If 1 and force then go ahead and create a new assembly if '1' in args.steps and args.force: data = ip.Assembly(assembly_name) else: data = ip.load_json(assembly_file) except IPyradWarningExit as inst: ## if no assembly is found then go ahead and make one if '1' not in args.steps: raise IPyradWarningExit(""" Error: Steps >1 ({}) requested but no current assembly found - {} """.format(args.steps, assembly_file)) else: ## create a new assembly object data = ip.Assembly(assembly_name) ## for entering some params... for param in parsedict: ## trap assignment of assembly_name since it is immutable. if param == str(0): ## only pass to set_params if user tried to change assembly_name ## it will raise an Exit error if parsedict[param] != data.name: data.set_params(param, parsedict[param]) else: ## all other params should be handled by set_params data.set_params(param, parsedict[param]) return data def parse_command_line(): """ Parse CLI args. Only three options now. """ ## create the parser parser = argparse.ArgumentParser( formatter_class=argparse.RawDescriptionHelpFormatter, epilog="""\n * Example command-line usage: ipyrad -n data ## create new file called params-data.txt ipyrad -p params-data.txt ## run ipyrad with settings in params file ipyrad -p params-data.txt -s 123 ## run only steps 1-3 of assembly. ipyrad -p params-data.txt -s 4567 ## run steps 4-7 of assembly. ipyrad -p params-data.txt -s 3 -f ## run step 3, overwrite existing data. * Preview mode: ipyrad -p params-data.txt -s --preview ## Run fast preview mode for testing * HPC parallelization ipyrad -p params-data.txt -s 3 --MPI ## access cores across multiple nodes * Results summary quick view ipyrad -p params-data.txt -r ## print summary stats to screen for 'data' * Run quietly ipyrad -p params.txt -q ## Run quietly, do not write output to std out * Branch assembly ipyrad -p params-data.txt -b newdata ## Create new branch of Assembly 'data' ## called 'newdata', which inherits ## stats/files from 'data'. * Get parameter info ipyrad -i ## Get a list of parameter names ipyrad -i 7 ## Get detailed info about a specific parameter * Documentation: http://ipyrad.readthedocs.org/en/latest/ """) ## add arguments parser.add_argument('-v', '--version', action='version', version=str(pkg_resources.get_distribution('ipyrad'))) parser.add_argument('-r', "--results", action='store_true', help="show results summary for Assembly in params.txt and exit") parser.add_argument('-f', "--force", action='store_true', help="force overwrite of existing data") parser.add_argument('-q', "--quiet", action='store_true', help="do not print to stderror or stdout.") parser.add_argument('-i', metavar="info", dest="info", type=str, nargs="?", default=False, help="get info about parameters") parser.add_argument('-n', metavar='new', dest="new", type=str, default=None, help="create new file 'params-{new}.txt' in current directory") parser.add_argument('-p', metavar='params', dest="params", type=str, default=None, help="path to params file for Assembly: params-{assembly_name}.txt") parser.add_argument('-b', metavar='branch', dest="branch", type=str, default=None, help="create a new branch of the Assembly as params-{branch}.txt") parser.add_argument('-s', metavar="steps", dest="steps", type=str, default="1234567", help="subset of assembly steps to perform (Default=1234567)") parser.add_argument("-c", metavar="cores", dest="cores", type=int, default=4, help="number of CPU cores to use (Default=4)") parser.add_argument("--MPI", action='store_true', help="connect to parallel CPUs across multiple nodes") parser.add_argument("--preview", action='store_true', help="run ipyrad in preview mode. Subset the input file so it'll run"\ + "quickly so you can verify everything is working") ## if no args then return help message if len(sys.argv) == 1: parser.print_help() sys.exit(1) ## parse args args = parser.parse_args() if not any(x in ["params", "new", "info"] for x in vars(args).keys()): print("Bad arguments: ipyrad command must include at least one of"\ +"`-p`, `-n` or `-i`\n") parser.print_help() sys.exit(1) return args def main(): """ main function """ ## turn off traceback for the CLI ip.__interactive__ = 0 ## parse params file input (returns to stdout if --help or --version) args = parse_command_line() ## create new paramsfile if -n if args.new: ## Create a tmp assembly and call write_params to write out ## default params.txt file try: tmpassembly = ip.Assembly(args.new, quiet=True) tmpassembly.write_params("params-{}.txt".format(args.new), force=args.force) except Exception as inst: print(inst) sys.exit(2) print("\n New file `params-{}.txt` created in {}\n".\ format(args.new, os.path.realpath(os.path.curdir))) sys.exit(2) ## if showing results or branching, do not do any steps and do not print header if any( [args.results, args.branch, args.info] ): args.steps = "" print("") else: header = \ "\n --------------------------------------------------"+\ "\n ipyrad [v.{}]".format(ip.__version__)+\ "\n Interactive assembly and analysis of RADseq data"+\ "\n --------------------------------------------------" print(header) if not args.info == False: if args.info: ip.paramsinfo(int(args.info)) else: ip.paramsinfo() sys.exit(1) ## create new Assembly or load existing Assembly, quit if args.results elif args.params: parsedict = parse_params(args) if args.results: showstats(parsedict) elif args.branch: branch_assembly(args, parsedict) else: ## run Assembly steps if args.steps: ## launch or load assembly with custom profile/pid data = getassembly(args, parsedict) ## store ipcluster info data._ipcluster["cores"] = args.cores if args.MPI: data._ipcluster["engines"] = "MPI" else: data._ipcluster["engines"] = "Local" ## launch ipcluster and register for later destruction data = ipcontroller_init(data) ## set to print headers data._headers = 1 ## run assembly steps steps = list(args.steps) data.run(steps=steps, force=args.force, preview=args.preview) if __name__ == "__main__": main()