annotate BSseeker2/galaxy/bs_seeker2_wrapper.py @ 1:8b26adf64adc draft default tip

V2.0.5

import tempfile

__author__ = 'pf'
from subprocess import Popen
from collections import defaultdict
import sys, shutil, os, re



BUILD = 'build'
ALIGN = 'align'
CALL_METHYLATION = 'call_methylation'

EXEC = 'exec'
EXEC_PATH = EXEC+'-path'
ARG_TYPES = [BUILD, ALIGN, CALL_METHYLATION, EXEC]

USAGE = """
%(script)s is a wrapper script for bs_seeker2-build.py and bs_seeker2-align.py that is intended to be used with the Galaxy web platform.
The script takes command line parameters and runs bs_seeker2-align.py and bs_seeker2-build.py, if neccessary.

The parameters that are related to bs_seeker2-build.py must be prefixed with --%(build_tag)s.
The parameters that are related to bs_seeker2-align.py must be prefixed with --%(align_tag)s.
Additionally, the path to BS-Seeker2 has to be specified via the --%(exec_path)s option.

For example:

    python %(script)s --%(exec_path)s /mnt/Data/UCLA/Matteo/BS-Seeker --build-f data/arabidopsis/genome/Arabidopsis.fa --align-i data/arabidopsis/BS6_N1try2L7_seq.txt.fa --align-o data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output

This will run build the genome in Arabidopsis.fa and put the indexes in a temporary directory. bs_seeker2-align.py will be run on the
newly created genome index. I.e. the following two commands will be run in a shell:

    python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-build.py --db /tmp/tmpg8Eq1o -f /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/genome/Arabidopsis.fa

    python /mnt/Data/UCLA/Matteo/BS-Seeker/bs_seeker2-align.py --db /tmp/tmpg8Eq1o -o /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa.test_output -i /mnt/Data/UCLA/Matteo/bck_BS-Seeker/data/arabidopsis/BS6_N1try2L7_seq.txt.fa -g Arabidopsis.fa


The temporary directory will be deleted after the wrapper exits.


If no options related to bs_seeker2-build are passed, no genome index will be built and the corresponding pre-built genome index will be used
instead. No temporary files and directories will be created.

""" % { 'script' : os.path.split(__file__)[1], 'build_tag' :BUILD, 'align_tag' : ALIGN, 'exec_path' : EXEC_PATH }


def error(msg):
    print >> sys.stderr, 'ERROR: %s' % msg
    exit(1)


if __name__ == '__main__':
    if len(sys.argv) == 1:
        error('No parameters\n\n'+USAGE)


    # Parse command line arguments
    args = defaultdict(dict)
    arg_key = None
    arg_val = None
    arg_type = None

    for arg in sys.argv[1:]:
        if arg.startswith('--'):
            try:
                arg_type, arg_key = re.match(r'--(\w+)(.*)', arg).groups()
                if arg_type not in ARG_TYPES:
                    raise Exception("Bad argument: %s. arg_type (%s) must be one of: %s." % (arg, arg_type, ', '.join(ARG_TYPES)))
                if not arg_key or arg_key[0] != '-':
                    raise Exception("Bad argument: %s. arg_key (%s) must start with - or --." % (arg, arg_key))
            except Exception, e:
                error(str(e) + '\n\n' + USAGE)
            args[arg_type][arg_key] = ''
        else:
            args[arg_type][arg_key] = arg

    path_to_bs_seeker = args.get('exec', {'-path' : None})['-path'] # return None when exec not found
    if path_to_bs_seeker is None:
        error('You have to specify the path to BS-Seeker2 via --%s\n\n' % EXEC_PATH + USAGE)

    tempdir = None
    def run_prog(prog, params):
        cwd, _ = os.path.split(__file__)
        cmd = 'python %(prog)s %(params)s' % {
                   'prog'   : os.path.join(cwd, prog),
                   'params' : ' '.join('%s %s' % (arg_key, arg_val) for arg_key, arg_val in params.items())
                   }
        print 'exec:', cmd

        return_code = Popen(args = cmd, shell = True).wait()
        if return_code:
            if tempdir:
                shutil.rmtree(tempdir)
            error("%s exit with error code %d" % (prog, return_code))
    tempdir = tempfile.mkdtemp()

    # bs_seeker2-build
    if BUILD in args:
        args[BUILD]['--db'] = tempdir
        args[ALIGN]['--db'] = tempdir
        run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-build.py'), args[BUILD])

    # bs_seeker2-align
    args[ALIGN]['--temp_dir'] = tempdir
    run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-align.py'), args[ALIGN])


    def getopt(h, k1, k2, default):
        return h.get(k1, h.get(k2, default))
    # bs_seeker2-call_methylation
    args[CALL_METHYLATION].update({  '-i'    : args[ALIGN]['--output'],
                                     '--db'  : os.path.join(args[ALIGN]['--db'],
                                    os.path.split(  getopt(args[ALIGN],'-g', '--genome', None))[1] +
                                    ('_rrbs_%s_%s' % (getopt(args[ALIGN], '-l', '--low', '40'),
                                                      getopt(args[ALIGN], '-u', '--up', '500'))
                                     if len(set(['-r', '--rrbs']) & set(args[ALIGN])) > 0 else '') +
                                    '_' + args[ALIGN]['--aligner'])
                                    })
    run_prog(os.path.join(path_to_bs_seeker, 'bs_seeker2-call_methylation.py'), args[CALL_METHYLATION])

    if tempdir:
        shutil.rmtree(tempdir)