import os import tasks import helpers # Config --------------------------------------------------------------------- # Set up command line option handling, logger creation, and load config file options = helpers.get_options() logger_proxy, logging_mutex = helpers.make_logger(options, __file__) config = yaml.load(open(options.config).read()) def report(result): """Wrapper around Result.report""" result.report(logger_proxy, logging_mutex) # Pipeline ------------------------------------------------------------------- @files(list(tasks.fastq_to_other_files(config, extension='.bowtie.sam'))) def map(infile, outfile): result = tasks.bowtie(infile, outfile, config) report(result) @transform(map, suffix('.bowtie.sam'), '.bowtie.sam.count') def count(infile, outfile): result = tasks.count(infile, outfile, config) report(result) # ---------------------------------------------------------------------------- helpers.run(options)
import helpers # Config --------------------------------------------------------------------- # Set up command line option handling, logger creation, and load config file options = helpers.get_options() logger_proxy, logging_mutex = helpers.make_logger(options, __file__) config = yaml.load(open(options.config).read()) def report(result): """Wrapper around Result.report""" result.report(logger_proxy, logging_mutex) # Pipeline ------------------------------------------------------------------- @files(list(tasks.fastq_to_other_files(config, extension='.clipped'))) def clip(infile, outfile): result = tasks.clip(infile, outfile, config) @transform(clip, suffix('.clipped'), '.clipped.bowtie.sam') def map(infile, outfile): result = tasks.bowtie(infile, outfile, config) report(result) @transform(map, suffix('.bowtie.sam'), '.bowtie.sam.count') def count(infile, outfile): result = tasks.count(infile, outfile, config) report(result)
import helpers # Config --------------------------------------------------------------------- # Set up command line option handling, logger creation, and load config file options = helpers.get_options() logger_proxy, logging_mutex = helpers.make_logger(options, __file__) config = yaml.load(open(options.config).read()) def report(result): """Wrapper around Result.report""" result.report(logger_proxy, logging_mutex) # Pipeline ------------------------------------------------------------------- @files(list(tasks.fastq_to_other_files(config, extension='.clipped'))) def clip(infile, outfile): result = tasks.clip(infile, outfile, config) @transform(clip, suffix('.clipped'), '.clipped.bowtie.sam') def map(infile, outfile): result = tasks.bowtie(infile, outfile, config) report(result) @transform(map, suffix('.bowtie.sam'), '.bowtie.sam.count') def count(infile, outfile): result = tasks.count(infile, outfile, config) report(result) # ----------------------------------------------------------------------------