new_snake

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Matthew Stone <mstone5@mgh.harvard.edu>
# Distributed under terms of the MIT license.

"""
Create template snakemake project directory
"""

import argparse
import os
import subprocess as sp


# Docstring template
SNAKEFILE_DOCSTRING = """{project}.snake
Matthew Stone <mstone5@mgh.harvard.edu>

{{doc}}
"""

# Rules template
SNAKEFILE_RULES = """configfile: 'config.yaml'

CHROMS = [str(x) for x in range(1, 23)] + 'X Y'.split()

rule all:
    input:
        pass
"""

# Full Snakefile template
SNAKEFILE_TEMPLATE = '"""\n{docstring}"""\n\n{rules}'
SNAKEFILE_TEMPLATE = SNAKEFILE_TEMPLATE.format(docstring=SNAKEFILE_DOCSTRING,
                                               rules=SNAKEFILE_RULES)

# cluster.yaml template
# Includes default LSF parameters and pattern for s/rulename/${rulename}
CLUSTER_TEMPLATE = """# LSF configuration
__default__:
    queue: normal
    sla: miket_sc
    log: logs/snakemake.out
    jobname: snakemake
rulename:
    queue: normal
    sla: miket_sc
    log: logs/rulename.out
    jobname: rulename
"""

CONFIG_TEMPLATE = """# Project constants
blacklist: /data/talkowski/rlc47/src/b37.lumpy.exclude.4-13.bed.gz
"""


def make_snake_project(project, symlinks):
    """
    Parameters
    ----------
    project : str
        Project directory name
    symlinks : list of str
        List of directories to symlink into project (absolute or relative)
    """

    if os.path.exists(project):
        raise Exception('Directory {} already exists'.format(project))

    # Create project directory
    os.mkdir(project)

    # Symlink in desired data directories and exclude from git
    GITIGNORE_TEMPLATE = "logs\n.gitignore"
    for symlink in symlinks:
        pathname = os.path.realpath(symlink)
        dirname = os.path.basename(pathname)
        os.symlink(pathname, os.path.join(project, dirname))
        GITIGNORE_TEMPLATE = GITIGNORE_TEMPLATE + '\n' + dirname

    # Create log directory for snakefile jobs
    os.chdir(project)
    os.mkdir('logs')
    os.mkdir('scripts')
    os.mkdir('data')

    # Create default snakefile named after project
    snakefile = open('Snakefile', 'w')
    template = SNAKEFILE_TEMPLATE.format(project=project)
    snakefile.write(template)
    snakefile.close()

    # Create cluster.yaml template
    cluster = open('cluster.yaml', 'w')
    cluster.write(CLUSTER_TEMPLATE)
    cluster.close()

    # Create config.yaml template
    config = open('config.yaml', 'w')
    config.write(CONFIG_TEMPLATE)
    config.close()

    # Create git repo
    sp.call('git init'.split())
    sp.call('git add Snakefile cluster.yaml config.yaml scripts data'.split())
    sp.call('git commit -m "Init"'.split())
    gitignore = open('.gitignore', 'w')
    gitignore.write(GITIGNORE_TEMPLATE)
    gitignore.close()


def main():
    parser = argparse.ArgumentParser(
        description=__doc__,
        formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('project', help='Project directory name')
    parser.add_argument('symlinks', nargs='*',
                        help='Files and directories to symlink into project')
    args = parser.parse_args()

    make_snake_project(args.project, args.symlinks)


if __name__ == '__main__':
    main()