--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sspace.py	Tue Sep 17 09:41:18 2013 -0400
@@ -0,0 +1,129 @@
+# -*- coding: utf-8 -*-
+"""
+SSPACE wrapper
+"""
+
+import logging
+import optparse
+import os
+import shutil
+import subprocess
+import tempfile
+
+
+def which(name, flags=os.X_OK):
+    """ Search PATH for executable files with the given name. """
+    result = []
+    exts = filter(None, os.environ.get('PATHEXT', '').split(os.pathsep))
+    path = os.environ.get('PATH', None)
+    if path is None:
+        return []
+    for p in os.environ.get('PATH', '').split(os.pathsep):
+        p = os.path.join(p, str(name))
+        if os.access(p, flags):
+            result.append(p)
+            for e in exts:
+                pext = p + e
+                if os.access(pext, flags):
+                    result.append(pext)
+    return result
+
+
+LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s'
+LOG_DATEFMT = '%Y-%m-%d %H:%M:%S'
+LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']
+
+
+def __main__():
+    """ main function """
+    parser = optparse.OptionParser()
+    parser.add_option('-c', dest='contigs', help='contigs mandatory (-s)')
+    parser.add_option('--r1', dest='reads1', help='')
+    parser.add_option('--r2', dest='reads2', help='')
+    parser.add_option('-i', dest='insert', type='int', help='')
+    parser.add_option('-e', dest='error', type='float', help='')
+    parser.add_option('-o', dest='orientation', choices=['FF', 'FR', 'RF', 'RR'], help='')
+    parser.add_option('-x', action='store_true', dest='extension', help='whether to extend the contigs (-x)')
+    parser.add_option('--minoverlap', dest='minoverlap', type='int', help='minoverlap (-m)')
+    parser.add_option('--numofreads', dest='numofreads', type='int', help='num of reads to call an extension (-o)')
+    parser.add_option('-t', dest='max_trim', type='int', help='maximum number of bases to trim on the contig end when all possibilities have been exhausted for an extension (-t)')
+    parser.add_option('-u', dest='unpaired', help='unpaired reads (-u, optional)')
+    parser.add_option('-r', dest='min_base_ratio', type='float', help='minimum base ratio used to accept a overhang consensus base (-r)')
+    parser.add_option('--minlink', dest='minlink', type='int', help='min link (-k)')
+    parser.add_option('--maxratio', dest='maxratio', type='float', help='max ratio (-a)')
+    parser.add_option('--contigoverlap', dest='contigoverlap', type='int', help='contigoverlap (-n)')
+    parser.add_option('--mincontig', dest='mincontig', type='int', help='mincontig (-z)')
+    parser.add_option('-T', dest='n_threads', type='int', help='number of threads to use in Bowtie (-T)')
+    parser.add_option('-p', dest='prefix', default='sspace_pre', help='prefix (-b)')
+    parser.add_option('--lib', dest='libraryname', default='galx', help='libraryfile')
+    parser.add_option('--fe', dest='finalevidence', help='')
+    parser.add_option('--fs', dest='finalscaffolds', help='')
+    parser.add_option('--lg', dest='logfile', help='')
+    parser.add_option('--summ', dest='summaryfile', help='')
+    parser.add_option('--loglevel', choices=LOG_LEVELS, help='logging level (default: INFO)', default='DEBUG')
+    (options, args) = parser.parse_args()
+    if len(args) > 0:
+        parser.error('Wrong number of arguments')
+    
+    log_level = getattr(logging, options.loglevel)
+    kwargs = {'format' : LOG_FORMAT,
+              'datefmt' : LOG_DATEFMT,
+              'level' : log_level}
+    if options.logfile:
+        kwargs['filename'] = options.logfile
+    logging.basicConfig(**kwargs)
+    logger = logging.getLogger('SSPACE scaffold assembly')
+    
+    logger.debug('Creating temp dir')
+    contigs = options.contigs
+    reads1 = options.reads1
+    reads2 = options.reads2
+    insert = options.insert
+    error = options.error
+    orientation = options.orientation
+    extension = '-x 1' if options.extension else ''
+    minoverlap = "-m %d" % options.minoverlap if options.minoverlap is not None else ''
+    numofreads = "-o %d" % options.numofreads if options.numofreads is not None else ''
+    max_trim = "-t %d" % options.max_trim if options.max_trim is not None else ''
+    unpaired = "-u %s" % options.unpaired if options.unpaired else ''
+    min_base_ratio = "-r %s" % options.min_base_ratio if options.min_base_ratio is not None else ''
+    minlink = "-k %d" % options.minlink if options.minlink is not None else ''
+    maxratio = "-a %s" % options.maxratio if options.maxratio is not None else ''
+    contigoverlap = "-n %d" % options.contigoverlap if options.contigoverlap is not None else ''
+    mincontig = "-z %d" % options.mincontig if options.mincontig is not None else ''
+    n_threads = "-T %d" % options.n_threads if options.n_threads is not None else ''
+    prefix = options.prefix
+    libraryname = options.libraryname
+    finalevidence = options.finalevidence
+    finalscaffolds = options.finalscaffolds
+    summaryfile = options.summaryfile
+    exe_name = "SSPACE_Basic_v2.0.pl"
+    
+    # Set library
+    outline = 'lib1 %s %s %d %s %s\n' % (reads1, reads2, insert, error, orientation)
+    with open(libraryname, 'w') as out:
+        out.write(outline)
+    
+    exe = which(exe_name, os.R_OK)
+    command = "perl %s -l %s -s %s %s %s %s %s %s %s %s %s %s %s %s -b %s" % (exe.pop(), libraryname, contigs, extension, minoverlap, numofreads, max_trim, unpaired, min_base_ratio, minlink, maxratio, contigoverlap, mincontig, n_threads, prefix)
+    wd = tempfile.mkdtemp()
+    try:
+        os.chdir(wd)
+        logger.info("SSPACE running")
+        logger.debug("executing %s" % command)
+        subprocess.check_call(args=command, shell=True)
+        
+        # Clean environment
+        with open("%s.logfile.txt" % os.path.join(wd, prefix), 'rb') as sspace_log_file:
+            logger.info("\n".join(["Log from SSPACE", sspace_log_file.read()]))
+        logger.info("Moving result files")
+        shutil.move("%s.final.evidence" % os.path.join(wd, prefix), finalevidence)
+        shutil.move("%s.final.scaffolds.fasta" % os.path.join(wd, prefix), finalscaffolds)
+        shutil.move("%s.summaryfile.txt" % os.path.join(wd, prefix), summaryfile)
+        logger.debug("Removing temp dir: %s" % wd)
+    finally:
+        shutil.rmtree(wd)
+
+
+if __name__ == "__main__":
+    __main__()