Python fastq_to_other_files Examples

Example #1

File: pipeline.py Project: carina28/pipeline-example

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)

Example #2

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)

Example #3

File: pipeline.py Project: boratonAJ/pipeline-example

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)
# ----------------------------------------------------------------------------