comparison tools/protein_analysis/seq_analysis_utils.py @ 9:e52220a9ddad draft

Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).

8:976a5f2833cd

def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
    sys.stderr.write("%s\n" % msg)
    sys.exit(error_level)

def fasta_iterator(filename, max_len=None, truncate=None):
    """Simple FASTA parser yielding tuples of (title, sequence) strings."""
    handle = open(filename)
    title, seq = "", ""

def run_jobs(jobs, threads, pause=10, verbose=False):
    """Takes list of cmd strings, returns dict with error levels."""
    pending = jobs[:]
    running = []
    results = {}
    while pending or running:
        #See if any have finished
        for (cmd, process) in running:
            return_code = process.poll() #non-blocking
            if return_code is not None:

9:e52220a9ddad

def stop_err(msg, error_level=1):
    """Print error message to stdout and quit with given error level."""
    sys.stderr.write("%s\n" % msg)
    sys.exit(error_level)

try:
    from multiprocessing import cpu_count
except ImportError:
    #Must be under Python 2.5, this is copied from multiprocessing:
    def cpu_count():
        """Returns the number of CPUs in the system."""
        if sys.platform == 'win32':
            try:
                num = int(os.environ['NUMBER_OF_PROCESSORS'])
            except (ValueError, KeyError):
                num = 0
        elif 'bsd' in sys.platform or sys.platform == 'darwin':
            comm = '/sbin/sysctl -n hw.ncpu'
            if sys.platform == 'darwin':
                comm = '/usr' + comm
                try:
                    with os.popen(comm) as p:
                        num = int(p.read())
                except ValueError:
                    num = 0
        else:
            try:
                num = os.sysconf('SC_NPROCESSORS_ONLN')
            except (ValueError, OSError, AttributeError):
                num = 0

        if num >= 1:
            return num
        else:
            raise NotImplementedError('cannot determine number of cpus')


def thread_count(command_line_arg, default=1):
    try:
        num = int(command_line_arg)
    except:
        num = default
    if num < 1:
        stop_err("Threads argument %r is not a positive integer" % command_line_arg)
    #Cap this with the pysical limit of the machine,
    try:
        num = min(num, cpu_count())
    except NotImplementedError:
        pass
    #For debugging,
    #hostname = os.environ.get("HOSTNAME", "this machine")
    #sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
    return num


def fasta_iterator(filename, max_len=None, truncate=None):
    """Simple FASTA parser yielding tuples of (title, sequence) strings."""
    handle = open(filename)
    title, seq = "", ""

def run_jobs(jobs, threads, pause=10, verbose=False):
    """Takes list of cmd strings, returns dict with error levels."""
    pending = jobs[:]
    running = []
    results = {}
    if threads == 1:
        #Special case this for speed, don't need the waits
        for cmd in jobs:
            results[cmd] = subprocess.call(cmd, shell=True)
        return results
    while pending or running:
        #See if any have finished
        for (cmd, process) in running:
            return_code = process.poll() #non-blocking
            if return_code is not None: